8A3H

Cellobiose-derived imidazole complex of the endoglucanase cel5A from Bacillus agaradhaerens at 0.97 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.118 
  • R-Value Work: 0.104 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Lateral Protonation of a Glycosidase Inhibitor. Structure of the Bacillus agaradhaerens Cel5A in Complex with a Cellobiose-Derived Imidazole at 0.97 A Resolution

Varrot, A.Schulein, M.Pipelier, M.Vasella, A.Davies, G.J.

(1999) J Am Chem Soc 121: 2621-2622


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ENDOGLUCANASE)A303Salipaludibacillus agaradhaerensMutation(s): 0 
Gene Names: cel5A
EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens)
Explore O85465 
Go to UniProtKB:  O85465
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85465
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IDC
Query on IDC

Download Ideal Coordinates CCD File 
D [auth A](5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside
C14 H22 N2 O9
CSXOUJBOYXGFCL-OFKZETBZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IDC Binding MOAD:  8A3H Ki: 8.80e+4 (nM) from 1 assay(s)
PDBBind:  8A3H Ki: 8.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.118 
  • R-Value Work: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.45α = 90
b = 69.88β = 90
c = 77.32γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-21
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary