MolNFT v1 · #38097 · protein

Crystal structure of bjp-1, a subclass B3 metallo-beta-lactamase of bradyrhizobium japonicum

2GMN: “Crystal structure of bjp-1, a subclass B3 metallo-beta-lactamase of bradyrhizobium japonicum”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.59). MolNFT v1 #38097 on GenesisL1: 3D structure, binding sites and…

PDB: 2GMN
Type: protein
Length: 528 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase
EC: 3.5.2.6
Ligands: ZN
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Metallo-beta-lactamase (EC 3.5.2.6)	protein	264	34% helix, 23% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 6 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	409	0.59	0.76	42	empty
2	123	0.43	0.76	21	ZN
3	100	0.42	0.77	22	ZN
4	131	0.40	0.74	27	empty

Interfaces

1 interface between chains.

A–B · 426 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2GMN · Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium… · 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
Elsewhere: RCSB PDB 2GMN · PDBe 2GMN

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