MolNFT v1 · #51429 · protein

Crystal structures of a benzoate CoA ligase from burkholderia xenovorans LB400

2V7B · Benzoate-coenzyme a ligase: “Crystal structures of a benzoate CoA ligase from burkholderia xenovorans LB400”. X-ray diffraction, 1 ligand (BEZ), 17 pockets (best druggability 0.75). MolNFT v1 #51429 on GenesisL1: 3D structure…

PDB: 2V7B
Type: protein
Length: 978 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Benzoate-coenzyme a ligase
EC: 6.2.1.25
UniProt: Q13WK3
Ligands: BEZ
Pockets: 17 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Benzoate-coenzyme a ligase (EC 6.2.1.25)	protein	489	34% helix, 26% strand	Q13WK3

Ligands and binding sites

BEZ · Benzoic acid · ligand · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.75	0.97	21	empty
2	71	0.73	0.97	20	empty
3	574	0.71	0.80	51	BEZ
4	583	0.71	0.79	59	BEZ
5	53	0.71	0.98	20	empty

Interfaces

1 interface between chains.

A–B · 1295 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

2V7B · Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400 · 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 Q13WK3
Elsewhere: RCSB PDB 2V7B · PDBe 2V7B · UniProt Q13WK3

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