8A3H

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

• PDB DOI: https://doi.org/10.2210/pdb8A3H/pdb

• Classification: HYDROLASE
• Organism(s): Salipaludibacillus agaradhaerens
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 1999-01-20 Released: 2000-01-21 
• Deposition Author(s): Varrot, A., Schulein, M., Pipelier, M., Vasella, A., Davies, G.J.

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Experimental Data Snapshot

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

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.16 kDa 
• Atom Count: 3,060 
• Modelled Residue Count: 300 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ENDOGLUCANASE)	A	303	Salipaludibacillus agaradhaerens	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens) Explore O85465  Go to UniProtKB:  O85465

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IDC	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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	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
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding 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 = 54.45	α = 90
b = 69.88	β = 90
c = 77.32	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-21 
Deposition Author(s): Varrot, A., Schulein, M., Pipelier, M., Vasella, A., Davies, G.J.

Revision History  

• 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
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary