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Crystal structure of metallo-beta-lactamase vim-1 in complex with ML302F inhibitor

Analyse Crystal structure of metallo-beta-lactamase vim-1 in complex with ML302F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N5H
Type: protein
Length: 234 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase vim-1
UniProt: Q9XAY4
Ligands: S3C, ZN
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase vim-1	protein	234	28% helix, 28% strand	Q9XAY4

Ligands and binding sites

S3C · (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A

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	257	0.58	0.79	30	ZN, S3C

Compared structures

5N5H · Crystal structure of metallo-beta-lactamase VIM-1 in complex with ML302F inhibitor · 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 Q9XAY4
Elsewhere: RCSB PDB 5N5H · PDBe 5N5H · UniProt Q9XAY4

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