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Crystal structure of the metallo-beta-lactamase VIM1 with 3193

Analyse Crystal structure of the metallo-beta-lactamase VIM1 with 3193 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8PGP
Type: protein
Length: 232 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 0.97
Source: Pseudomonas aeruginosa
Molecule: Beta-lactamase VIM-1
UniProt: Q9XAY4
Ligands: YSR, ZN
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · resolution 0.97 · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase VIM-1	protein	232	27% helix, 29% strand	Q9XAY4

Ligands and binding sites

YSR · 7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-cyano-4-(methylsulfonylamino)phenyl]-1~{H}-indole-2-carboxylic 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	184	0.53	0.79	27	YSR

Analyse

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Every structure of UniProt Q9XAY4
Elsewhere: RCSB PDB 8PGP · PDBe 8PGP · UniProt Q9XAY4

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