MolNFT v1 · #137473 · protein

Crystal structure of beta-lactamase from burkholderia phymatum

5VPQ: “Crystal structure of beta-lactamase from burkholderia phymatum”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.52). MolNFT v1 #137473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VPQ
Type: protein
Length: 547 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: B2JET9
Ligands: PO4
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	277	45% helix, 19% strand	B2JET9
B	Beta-lactamase (EC 3.5.2.6)	protein	270	45% helix, 17% strand	B2JET9

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.52	0.85	26	empty
2	224	0.50	0.76	33	EDO
3	67	0.30	0.75	15	empty
4	62	0.30	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 487 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5VPQ · Crystal structure of beta-lactamase from Burkholderia phymatum · 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 B2JET9
Elsewhere: RCSB PDB 5VPQ · PDBe 5VPQ · UniProt B2JET9

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