MolNFT v1 · #176666 · protein

Crystal structure of vim-2 mbl in complex with 1-propyl-1H-imidazole- 2-carboxylic acid

7DU1 · Beta-lactamase class B vim-2: “Crystal structure of vim-2 mbl in complex with 1-propyl-1H-imidazole- 2-carboxylic acid”. X-ray diffraction, 2 ligands (HKR, ZN), 1 pocket (best druggability 0.72). MolNFT v1 #176666 on GenesisL1: 3D…

PDB: 7DU1
Type: protein
Length: 462 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase class B vim-2
UniProt: Q9K2N0
Ligands: HKR, ZN
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

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

Ligands and binding sites

HKR · 1-propylimidazole-2-carboxylic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 6 copies · chains A, B
FMT · Formic acid · additive · 4 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	545	0.72	0.81	52	HKR, ZN

Interfaces

1 interface between chains.

A–B · 596 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7DU1 · Crystal structure of VIM-2 MBL in complex with 1-propyl-1H-imidazole-2-carboxylic acid · 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 7DU1 · PDBe 7DU1 · UniProt Q9K2N0

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