8BQB

CjCel5C endo-glucanase bound to CB396 covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8BQB/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus Ueda107
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2022-11-20 Released: 2023-11-29 
• Deposition Author(s): McGregor, N.G.S., de Boer, C., Overkleeft, H.S., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 

Literature

Dissection of a Native Bacterial Xyloglucan-degrading System using Activity-Based Probes

McGregor, N.G.S., de Boer, C., Foucart, Q., Beenakker, T., Willems, L., Overkleeft, H.S., Davies, G.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 121.73 kDa 
• Atom Count: 8,134 
• Modelled Residue Count: 989 
• Deposited Residue Count: 1,038 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase, putative, cel5C	A, B, C	346	Cellvibrio japonicus Ueda107	Mutation(s): 0  Gene Names: cel5C
UniProt
Find proteins for B3PF55 (Cellvibrio japonicus (strain Ueda107)) Explore B3PF55  Go to UniProtKB:  B3PF55

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YLL (Subject of Investigation/LOI)	D [auth A], F [auth B], I [auth C]	(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL C7 H14 O6 QFYQIWDMMSKNFF-NYLBLOMBSA-N
BGC (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.441	α = 90
b = 176.159	β = 90
c = 115.701	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): McGregor, N.G.S., de Boer, C., Overkleeft, H.S., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R001162/1
European Research Council (ERC)	European Union	2020-SyG-951231

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release