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Crystal structure of PBGH5A, a glycoside hydrolase family 5 enzyme from prevotella bryantii B14

Analyse Crystal structure of PBGH5A, a glycoside hydrolase family 5 enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VDH
Type: protein
Length: 693 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-1,4-endoglucanase
UniProt: O06842
Ligands: CL
Pockets: 1 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B-1,4-endoglucanase	protein	346	44% helix, 13% strand	O06842
B	B-1,4-endoglucanase	protein	347	44% helix, 13% strand	O06842

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1108	0.84	0.85	101	CL

Interfaces

1 interface between chains.

A–B · 668 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 modified (engineered).

Compared structures

3VDH · Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella… · the same entry in another collection · 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 O06842
Elsewhere: RCSB PDB 3VDH · PDBe 3VDH · UniProt O06842

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