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Crystal structure of the metallo-beta-lactamase vim-5

Analyse Crystal structure of the metallo-beta-lactamase vim-5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5A87
Type: protein
Length: 464 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase vim-5
EC: 3.5.2.6
UniProt: Q4ZE97
Ligands: ZN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallo-beta-lactamase vim-5 (EC 3.5.2.6)	protein	230	27% helix, 29% strand	Q4ZE97
B	Metallo-beta-lactamase vim-5 (EC 3.5.2.6)	protein	234	26% helix, 28% strand	Q4ZE97

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.72	0.83	64	GOL
2	85	0.42	0.79	26	empty
3	66	0.38	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 627 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5A87 · Crystal structure of the metallo-beta-lactamase VIM-5 · 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 Q4ZE97
Elsewhere: RCSB PDB 5A87 · PDBe 5A87 · UniProt Q4ZE97

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