1H5V

Thiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic Resolution Structure of Endoglucanase Cel5A in Complex with Methyl 4,4II,4III,4Iv-Tetrathio-Alpha-Cellopentoside Highlights the Alternative Binding Modes Targeted by Substrate Mimics

Varrot, A.Schulein, M.Fruchard, S.Driguez, H.Davies, G.J.

(2001) Acta Crystallogr.,Sect.D 57: 1739


  • PubMed Abstract: 
  • Many three-dimensional structures of retaining beta-D-glycoside hydrolases have been determined, yet oligosaccharide complexes in which the ligand spans the catalytic centre are rare. Those that have been reported so far have revealed two modes of bi ...

    Many three-dimensional structures of retaining beta-D-glycoside hydrolases have been determined, yet oligosaccharide complexes in which the ligand spans the catalytic centre are rare. Those that have been reported so far have revealed two modes of binding: those in which the substrate adopts a distorted skew-boat or envelope conformation in the -1 subsite, reflecting the distortion observed during the catalytic cycle, and those which bypass the true catalytic centre and thus lie in a non-productive manner across the -1 subsite. The three-dimensional structure of a retaining endocellulase, Bacillus agaradhaerens Cel5A, in complex with methyl 4,4(II),4(III),4(IV)-tetrathio-alpha-cellopentoside falls into this latter category. The 1.1 A structure reveals the binding of five pyranosides, all in the (4)C(1) chair conformation, occupying the -3, -2, +1 and +2 subsites whilst evading the catalytic machinery located in the true -1 subsite. Such binding is in marked contrast to the structure of another retaining endocellulase, the Fusarium oxysporum Cel7B, the identical ligand in which displayed a distorted skew-boat conformation at the active centre. These two binding modes may reflect different steps in the binding and catalytic process.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York Y010 5DD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOGLUCANASE 5A
A
304Bacillus agaradhaerensGene Names: cel5A
EC: 3.2.1.4
Find proteins for O85465 (Bacillus agaradhaerens)
Go to UniProtKB:  O85465
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSG
Query on SSG

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A
1,4-DEOXY-1,4-DITHIO-BETA-D-GLUCOPYRANOSE
C6 H12 O4 S2
MUOMBPNNVXJUGT-UKFBFLRUSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

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A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MA3
Query on MA3

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A
O1-METHYL-4-DEOXY-4-THIO-ALPHA-D-GLUCOSE
C7 H14 O5 S
PFROTWRHYMLGHR-GKHCUFPYSA-N
 Ligand Interaction
SGC
Query on SGC

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A
4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE
C6 H12 O5 S
KGSURTOFVLAWDC-QZABAPFNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.120 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.169α = 90.00
b = 75.169β = 90.00
c = 135.471γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance