MolNFT v1 · #126077 · protein

Crystal structure of metallo-beta-lactamase spm-1 with Y58C mutation

5LS3 · Beta-lactamase imp-1: “Crystal structure of metallo-beta-lactamase spm-1 with Y58C mutation”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.74). MolNFT v1 #126077 on GenesisL1: 3D structure, binding sites and…

PDB: 5LS3
Type: protein
Length: 484 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase imp-1
EC: 3.5.2.6
UniProt: Q8G9Q0
Ligands: ZN
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Beta-lactamase imp-1 (EC 3.5.2.6)	protein	245	33% helix, 28% strand	Q8G9Q0
A	Beta-lactamase imp-1 (EC 3.5.2.6)	protein	239	31% helix, 28% strand	Q8G9Q0

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains B, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	699	0.74	0.80	64	ZN
2	255	0.66	0.83	38	ZN
3	250	0.53	0.76	25	empty

Interfaces

1 interface between chains.

B–A · 524 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5LS3 · Crystal structure of metallo-beta-lactamase SPM-1 with Y58C mutation · the same entry in another collection · chain B against B, 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 Q8G9Q0
Elsewhere: RCSB PDB 5LS3 · PDBe 5LS3 · UniProt Q8G9Q0

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