Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) β-glucosidase Download PDB file

Protein: Beta-glucosidase

Organism: Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)

Lenght: 441

UniprotID: Q82BV6 (Download sequence)

Template: 1NP2:A (49.55%) | [φ,ψ] plot


Loop | bend | hydrogen bonded turn', 'default', '', '1', '400', 'methionine');" onmouseout="hideAminoAcid('M', 'M1')" onmouseover="showAminoAcid('M1'); selectID(glviewer,1)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 1

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="M Local position: 1 Global position: 400" > M
Loop | bend | hydrogen bonded turn', 'default', '', '2', '401', 'isoleucine');" onmouseout="hideAminoAcid('I', 'I2')" onmouseover="showAminoAcid('I2'); selectID(glviewer,2)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 2

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="I Local position: 2 Global position: 401" > I
Loop | bend | hydrogen bonded turn', 'default', '', '3', '402', 'arginine');" onmouseout="hideAminoAcid('R', 'R3')" onmouseover="showAminoAcid('R3'); selectID(glviewer,3)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 3

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="R Local position: 3 Global position: 402" > R
Loop | bend | hydrogen bonded turn', 'default', '', '4', '403', 'arginine');" onmouseout="hideAminoAcid('R', 'R4')" onmouseover="showAminoAcid('R4'); selectID(glviewer,4)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 4

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="R Local position: 4 Global position: 403" > R
Loop | bend | hydrogen bonded turn', 'info', '', '36', '460', 'glutamic acid');" onmouseout="hideAminoAcid('E', 'E36')" onmouseover="showAminoAcid('E36'); selectID(glviewer,36)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 36

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="E Local position: 36 Global position: 460" > E
Loop | bend | hydrogen bonded turn', 'info', '', '37', '461', 'proline');" onmouseout="hideAminoAcid('P', 'P37')" onmouseover="showAminoAcid('P37'); selectID(glviewer,37)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 37

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="P Local position: 37 Global position: 461" > P
Loop | bend | hydrogen bonded turn', 'default', '', '71', '549', 'alanine');" onmouseout="hideAminoAcid('A', 'A71')" onmouseover="showAminoAcid('A71'); selectID(glviewer,71)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 71

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="A Local position: 71 Global position: 549" > A
Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '72', '550', 'leucine');" onmouseout="hideAminoAcid('L', 'L72')" onmouseover="showAminoAcid('L72'); selectID(glviewer,72)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 72

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="L Local position: 72 Global position: 550" > L
Loop | bend | hydrogen bonded turn', 'info', '', '106', '634', 'leucine');" onmouseout="hideAminoAcid('L', 'L106')" onmouseover="showAminoAcid('L106'); selectID(glviewer,106)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 106

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="L Local position: 106 Global position: 634" > L
Loop | bend | hydrogen bonded turn', 'info', '', '107', '635', 'cysteine');" onmouseout="hideAminoAcid('C', 'C107')" onmouseover="showAminoAcid('C107'); selectID(glviewer,107)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 107

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="C Local position: 107 Global position: 635" > C
Loop | bend | hydrogen bonded turn', 'info', '', '141', '711', 'alanine');" onmouseout="hideAminoAcid('A', 'A141')" onmouseover="showAminoAcid('A141'); selectID(glviewer,141)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 141

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="A Local position: 141 Global position: 711" > A
Loop | bend | hydrogen bonded turn', 'default', '', '142', '712', 'alanine');" onmouseout="hideAminoAcid('A', 'A142')" onmouseover="showAminoAcid('A142'); selectID(glviewer,142)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 142

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="A Local position: 142 Global position: 712" > A
Loop | bend | hydrogen bonded turn', 'danger', ' coevo_2_inactive', '176', '788', 'proline');" onmouseout="hideAminoAcid('P', 'P176')" onmouseover="showAminoAcid('P176'); selectID(glviewer,176)" class="btn btn-danger coevo_2_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 176

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="P Local position: 176 Global position: 788" > P
Loop | bend | hydrogen bonded turn', 'info', '', '177', '790', 'glycine');" onmouseout="hideAminoAcid('G', 'G177')" onmouseover="showAminoAcid('G177'); selectID(glviewer,177)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 177

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="G Local position: 177 Global position: 790" > G
Loop | bend | hydrogen bonded turn', 'danger', ' coevo_1_inactive', '211', '949', 'glycine');" onmouseout="hideAminoAcid('G', 'G211')" onmouseover="showAminoAcid('G211'); selectID(glviewer,211)" class="btn btn-danger coevo_1_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 211

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="G Local position: 211 Global position: 949" > G
Loop | bend | hydrogen bonded turn', 'default', '', '212', '950', 'isoleucine');" onmouseout="hideAminoAcid('I', 'I212')" onmouseover="showAminoAcid('I212'); selectID(glviewer,212)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 212

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="I Local position: 212 Global position: 950" > I
Loop | bend | hydrogen bonded turn', 'info', ' coevo_2_inactive', '246', '1200', 'proline');" onmouseout="hideAminoAcid('P', 'P246')" onmouseover="showAminoAcid('P246'); selectID(glviewer,246)" class="btn btn-info coevo_2_inactive conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 246

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="P Local position: 246 Global position: 1200" > P
Loop | bend | hydrogen bonded turn', 'default', '', '247', '1201', 'leucine');" onmouseout="hideAminoAcid('L', 'L247')" onmouseover="showAminoAcid('L247'); selectID(glviewer,247)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 247

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="L Local position: 247 Global position: 1201" > L
Loop | bend | hydrogen bonded turn', 'info', '', '281', '1401', 'tyrosine');" onmouseout="hideAminoAcid('Y', 'Y281')" onmouseover="showAminoAcid('Y281'); selectID(glviewer,281)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 281

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="Y Local position: 281 Global position: 1401" > Y
Loop | bend | hydrogen bonded turn', 'danger', ' coevo_2_inactive', '282', '1402', 'glycine');" onmouseout="hideAminoAcid('G', 'G282')" onmouseover="showAminoAcid('G282'); selectID(glviewer,282)" class="btn btn-danger coevo_2_inactive conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 282

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="G Local position: 282 Global position: 1402" > G
Loop | bend | hydrogen bonded turn', 'default', '', '316', '1493', 'glutamic acid');" onmouseout="hideAminoAcid('E', 'E316')" onmouseover="showAminoAcid('E316'); selectID(glviewer,316)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 316

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="E Local position: 316 Global position: 1493" > E
Loop | bend | hydrogen bonded turn', 'default', '', '317', '1494', 'isoleucine');" onmouseout="hideAminoAcid('I', 'I317')" onmouseover="showAminoAcid('I317'); selectID(glviewer,317)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 317

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="I Local position: 317 Global position: 1494" > I
Loop | bend | hydrogen bonded turn', 'info', '', '351', '1562', 'proline');" onmouseout="hideAminoAcid('P', 'P351')" onmouseover="showAminoAcid('P351'); selectID(glviewer,351)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 351

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="P Local position: 351 Global position: 1562" > P
Loop | bend | hydrogen bonded turn', 'default', '', '352', '1563', 'isoleucine');" onmouseout="hideAminoAcid('I', 'I352')" onmouseover="showAminoAcid('I352'); selectID(glviewer,352)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 352

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="I Local position: 352 Global position: 1563" > I
Loop | bend | hydrogen bonded turn', 'default', '', '386', '1672', 'alanine');" onmouseout="hideAminoAcid('A', 'A386')" onmouseover="showAminoAcid('A386'); selectID(glviewer,386)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 386

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="A Local position: 386 Global position: 1672" > A
Loop | bend | hydrogen bonded turn', 'danger', '', '387', '1674', 'glycine');" onmouseout="hideAminoAcid('G', 'G387')" onmouseover="showAminoAcid('G387'); selectID(glviewer,387)" class="btn btn-danger conserved80_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 387

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="G Local position: 387 Global position: 1674" > G
Loop | bend | hydrogen bonded turn', 'default', '', '421', '1798', 'threonine');" onmouseout="hideAminoAcid('T', 'T421')" onmouseover="showAminoAcid('T421'); selectID(glviewer,421)" class="btn btn-default

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 421

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="T Local position: 421 Global position: 1798" > T
Loop | bend | hydrogen bonded turn', 'info', '', '422', '1800', 'leucine');" onmouseout="hideAminoAcid('L', 'L422')" onmouseover="showAminoAcid('L422'); selectID(glviewer,422)" class="btn btn-info conserved50_active

A PHP Error was encountered

Severity: Warning

Message: Uninitialized string offset 422

Filename: views/view.php

Line Number: 255

Backtrace:

File: /scratch/html/glutantbase/application/views/view.php
Line: 255
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

ss_loop_inactive" style="" title="L Local position: 422 Global position: 1800" > L

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 -2.93 -2.50 0.43 ΔAffinity < 0 x
1-3 -2.30 -1.82 0.48 ΔAffinity < 0 x
1-10 -1.45 -0.98 0.47 ΔAffinity < 0 x

| Glucose docking

Poses (avg) Affinity (wild) Affinity (mutant) ΔAffinity ΔAffinity expected Status
1 -2.93 -6.00 -3.07 ΔAffinity > 0 x
1-3 -2.30 -5.86 -3.56 ΔAffinity > 0 x
1-10 -5.35 -5.45 -0.1 ΔAffinity > 0 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.