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Crystal structure of the metallo-beta-lactamase VIM2 with 139

Analyse Crystal structure of the metallo-beta-lactamase VIM2 with 139 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AFX
Type: protein
Length: 463 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase vim-2
UniProt: Q9K2N0
Ligands: R9K, ZN
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase vim-2	protein	231	27% helix, 29% strand	Q9K2N0
B	Beta-lactamase vim-2	protein	232	27% helix, 29% strand	Q9K2N0

Ligands and binding sites

R9K · 3-(2-chlorophenyl)-7-methyl-1~{H}-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 6 copies · chains A, B
FMT · Formic acid · additive · 6 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	542	0.70	0.79	51	R9K, ZN

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7AFX · Crystal structure of the metallo-beta-lactamase VIM2 with 139 · 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 Q9K2N0
Elsewhere: RCSB PDB 7AFX · PDBe 7AFX · UniProt Q9K2N0

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