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Crystal structure of vim-1 metallo-beta-lactamase in complex with hydrolysed meropenem

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

PDB: 5N5I
Type: protein
Length: 232 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase vim-1
UniProt: Q9XAY4
Ligands: LMP, ZN
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase vim-1	protein	232	28% helix, 29% strand	Q9XAY4

Ligands and binding sites

LMP · (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · 3 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	221	0.53	0.77	25	ZN, LMP

Compared structures

5N5I · Crystal Structure of VIM-1 metallo-beta-lactamase in complex with hydrolysed meropenem · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q9XAY4
Elsewhere: RCSB PDB 5N5I · PDBe 5N5I · UniProt Q9XAY4

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