› 8oz1

X-ray diffraction
1.3Å resolution

CjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor

Released:
DOI: 10.2210/pdb8oz1/pdb
PDB entry 8oz1 coloured by chain, front view.
PDB entry 8oz1 coloured by chain, side view.
PDB entry 8oz1 coloured by chain, top view.
Source organism: Cellvibrio japonicus Ueda107
Primary publication:
A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System.
McGregor NGS, de Boer C, Foucart QPO, Beenakker T, Offen WA, Codée JDC, Willems LI, Overkleeft HS, Davies GJ
ACS Cent Sci 9 2306-2314 (2023)
PMID: 38161374

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109886 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycoside hydrolase family 5 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 396 amino acids
Theoretical weight: 44.4 KDa
Source organism: Cellvibrio japonicus Ueda107
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B3PD52 (Residues: 96-468; Coverage: 80%)
Gene names: CJA_3010, cel5D
Sequence domains: Cellulase (glycosyl hydrolase family 5)

Ligands and Environments

4 bound ligands:
Ligand BO3 1 x BO3
Ligand RBH 1 x RBH
Ligand YLL 1 x YLL
Ligand XYS 1 x XYS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 52.36Å b: 57.132Å c: 65.951Å
α: 90° β: 98.528° γ: 90°
R-values:
R R work R free
0.136 0.134 0.169
Expression system: Escherichia coli BL21(DE3)

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