MolNFT v1 · #87363 · protein

Crystal structure of the metallo-beta-lactamase vim-2

4BZ3: “Crystal structure of the metallo-beta-lactamase vim-2”. X-ray diffraction, 2 ligands (ZN, NA), 1 pocket (best druggability 0.69). MolNFT v1 #87363 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BZ3
Type: protein
Length: 463 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase vim-2
EC: 3.5.2.6
UniProt: Q9K2N0
Ligands: ZN, NA
Pockets: 1 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase vim-2 (EC 3.5.2.6)	protein	231	27% helix, 29% strand	Q9K2N0
B	Beta-lactamase vim-2 (EC 3.5.2.6)	protein	232	27% helix, 28% strand	Q9K2N0

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
FMT · Formic acid · additive · 5 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	443	0.69	0.80	56	FMT, ZN

Interfaces

1 interface between chains.

A–B · 595 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4BZ3 · Crystal structure of the metallo-beta-lactamase VIM-2 · 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 4BZ3 · PDBe 4BZ3 · UniProt Q9K2N0

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