Sinorhizobium meliloti (strain SM11) β-glucosidase Download PDB file

Protein: Beta-glucosidase

Organism: Sinorhizobium meliloti (strain SM11)

Lenght: 458

UniprotID: F7X9K8 (Download sequence)

Template: 1QOX:A (47.51%) | [φ,ψ] plot

Amino acid:

Local position¹:

Global position²:

Conserved > 80%:

Conserved 50-79%:

Secondary structure:

Co-evoluted network:

Mutation predicted:

Co-evolution network³

Residue	Community	Network

¹ Residue Corresponding position in the amino acids sequence.

² We performed multiple alignment between all GH1 beta-glucosidases sequences using Clustal omega (default parameters). We collected the amino acids that appear in more than 50% of the sequences and more than 80% of the sequences.

³ Co-evolution network was generated using PFSTATS and family GH1 sequences obtained from PFAM. Amino acid residues edges represent correlation links between them.

Acid/base catalytic
Conserved (50-79%)
Conserved (> 80%)
Extrapoled mutation
Catalytic pocket (0-6.5Å from ligand)

Extrapoled mutations

| Cellobiose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-4.90	1.13	ΔAffinity < 0	x
1-3	-5.72	-4.43	1.29	ΔAffinity < 0	x
1-10	-4.49	-3.	1.49	ΔAffinity < 0	x

| Glucose docking

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-5.60	0.43	ΔAffinity > 0	✓
1-3	-5.72	-5.43	0.29	ΔAffinity > 0	✓
1-10			0	ΔAffinity > 0	x

| Cellobiose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 9

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 8

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-6.20	-0.17	ΔAffinity < 0	✓
1-3	-5.72	-5.73	-0.010000000000001	ΔAffinity < 0	✓
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 391 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 391 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 392 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 392 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity < 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

| Glucose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 11

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 10

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-5.70	0.33	ΔAffinity > 0	✓
1-3	-5.72	-5.43	0.29	ΔAffinity > 0	✓
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 445 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 445 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 446 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 446 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity > 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

| Cellobiose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 9

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 8

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-6.10	-0.069999999999999	ΔAffinity < 0	✓
1-3	-5.72	-5.88	-0.16	ΔAffinity < 0	✓
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 391 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 391 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 392 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 392 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity < 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

| Glucose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 11

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 10

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-5.67	0.36	ΔAffinity > 0	✓
1-3	-5.72	-5.36	0.36	ΔAffinity > 0	✓
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 445 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 445 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 446 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 446 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity > 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

| Cellobiose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 9

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 8

Filename: views/view.php

Line Number: 389

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 389
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-4.17	1.86	ΔAffinity < 0	x
1-3	-5.72	-3.28	2.44	ΔAffinity < 0	x
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 391 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 391 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 392 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 392 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 393 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 393 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity < 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 9 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 8 Filename: views/view.php Line Number: 395 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 395 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

| Glucose docking

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 11

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: Undefined array key 10

Filename: views/view.php

Line Number: 443

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 443
Function: _error_handler

File: /scratch/html/glutantbase/application/libraries/Template.php
Line: 13
Function: view

File: /scratch/html/glutantbase/application/controllers/Protein.php
Line: 188
Function: show

File: /scratch/html/glutantbase/index.php
Line: 315
Function: require_once

bg-danger">

Poses (avg)	Affinity (wild)	Affinity (mutant)	ΔAffinity	ΔAffinity expected	Status
1	-6.03	-5.70	0.33	ΔAffinity > 0	✓
1-3	-5.72	-5.58	0.14	ΔAffinity > 0	✓
1-10	A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 445 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 445 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 446 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 446 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 447 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 447 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once 0	ΔAffinity > 0	A PHP Error was encountered Severity: Warning Message: Undefined array key 11 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once A PHP Error was encountered Severity: Warning Message: Undefined array key 10 Filename: views/view.php Line Number: 449 Backtrace: File: /scratch/html/glutantbase/application/views/view.php Line: 449 Function: _error_handler File: /scratch/html/glutantbase/application/libraries/Template.php Line: 13 Function: view File: /scratch/html/glutantbase/application/controllers/Protein.php Line: 188 Function: show File: /scratch/html/glutantbase/index.php Line: 315 Function: require_once x

Methodology

Comparative modeling

Three-dimensional structures were modeled by homology using MODELLER. Sequences were collected in UniProt. We searched for the E.C. number of beta-glucosidases (3.2.1.21) and collected sequences of family GH1 (~3000). For each sequence, we selected the structure of highest identity using BLAST against the PDB database to be used as a template. Sequences with identity lower than 25% were discarded. 100 models were constructed for each sequence. The best model was selected using the lowest value of the DOPE score. Mutants were modeled using MODELLER's mutation script. The mutations were based on beneficial mutations described in the literature.

Minimization

PDB models were minimized using AMBER tools. We performed 1000 steps of minimization in the vacuum (parameters: imin=1, maxcyc=1000, ncyc=750, cut=10.0, ntb=0, igb=0).

Multiple alignment

We performed multiple alignment using Clustal Omega (default parameters). We used Python scripts to detect conservation.

Docking

We performed docking of glucose (product) and cellobiose (substrate) for wild and mutant beta-glucosidases using AutoDock Vina (parameters: exhaustiveness = 20; num_modes = 10). The box center was defined using the median coordinate of the last atom of the two catalytic glutamates. The experiment was performed in triplicate. We collected ten poses for each docking and analyzed the average of affinity energies predicted by the software for (i) pose 1, (ii) poses 1-3, and (iii) poses 1-10.

Sinorhizobium meliloti (strain SM11) β-glucosidase Download PDB file

Extrapoled mutations

H186F | Cellobiose docking

H186F | Glucose docking

A405V | Cellobiose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A405V | Glucose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

H230T | Cellobiose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

H230T | Glucose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

E101K | Cellobiose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

E101K | Glucose docking

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

A PHP Error was encountered

Methodology

Comparative modeling

Minimization

Multiple alignment

Docking

| Cellobiose docking

| Glucose docking

| Cellobiose docking

| Glucose docking

| Cellobiose docking

| Glucose docking

| Cellobiose docking

| Glucose docking