Sinorhizobium fredii USDA 205 β-glucosidase Download PDB file

Protein: Beta-glucosidase

Organism: Sinorhizobium fredii USDA 205

Lenght: 490

UniprotID: A0A0T6ZU64 (Download sequence)

Template: 1QOX:A (47.37%) | [φ,ψ] plot



Acid/base catalytic
Conserved (50-79%)
Conserved (> 80%)
Extrapoled mutation
Catalytic pocket (0-6.5Å from ligand)
α-helix | 3-helix | π-helix
β-bridge | β-ladder | β-strand
Loop | bend | hydrogen bonded turn
Community 1
Community 2

Extrapoled mutations

| Cellobiose docking

Poses (avg) Affinity (wild) Affinity (mutant) ΔAffinity ΔAffinity expected Status
1 -5.23 -5.73 -0.5 ΔAffinity < 0
1-3 -4.63 -5.20 -0.57 ΔAffinity < 0
1-10 -3.86 -4. -0.14 ΔAffinity < 0

| Glucose docking

Poses (avg) Affinity (wild) Affinity (mutant) ΔAffinity ΔAffinity expected Status
1 -5.23 -6.20 -0.97 ΔAffinity > 0 x
1-3 -4.63 -6.07 -1.44 ΔAffinity > 0 x
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 -5.23 -5.13 0.1 ΔAffinity < 0 x
1-3 -4.63 -4.74 -0.11 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 -5.23 -6.20 -0.97 ΔAffinity > 0 x
1-3 -4.63 -6.13 -1.5 ΔAffinity > 0 x
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 -5.23 -5.07 0.16 ΔAffinity < 0 x
1-3 -4.63 -4.69 -0.06 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 -5.23 -6.20 -0.97 ΔAffinity > 0 x
1-3 -4.63 -6.09 -1.46 ΔAffinity > 0 x
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 -5.23 -5.47 -0.24 ΔAffinity < 0
1-3 -4.63 -5.08 -0.45 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 -5.23 -6.20 -0.97 ΔAffinity > 0 x
1-3 -4.63 -6.03 -1.4 ΔAffinity > 0 x
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.