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Crystal structures of clostridium thermocellum xyloglucanase

Analyse Crystal structures of clostridium thermocellum xyloglucanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CN3
Type: protein
Length: 1,456 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-1,4-xyloglucan hydrolase
EC: 3.2.1.151
UniProt: Q70DK5
Ligands: BGC, XYS, GAL, GLC, CA
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-1,4-xyloglucan hydrolase (EC 3.2.1.151)	protein	728	3% helix, 39% strand	Q70DK5

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 12 copies · chains A, B
XYS · alpha-D-xylopyranose · sugar · 12 copies · chains A, B
GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B
GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	863	0.82	0.84	83	CA
2	534	0.81	0.87	45	CA
3	847	0.77	0.81	92	BGC, XYS, GLC
4	418	0.74	0.84	53	empty
5	481	0.66	0.78	46	BGC, XYS, GLC

Interfaces

1 interface between chains.

A–B · 353 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2CN3 · Crystal Structures of Clostridium thermocellum Xyloglucanase · the same entry in another collection · chain A against A, TM-score 1.00
Q70DK5 · AlphaFold monomer V2.0 prediction for xyloglucanase XGH74A (Q70DK5) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q70DK5
Elsewhere: RCSB PDB 2CN3 · PDBe 2CN3 · UniProt Q70DK5

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