MolNFT v1 · #113974 · protein

Crystal structure of metallo-beta-lactamase smb-1 bound to L-captopril

5AYA: “Crystal structure of metallo-beta-lactamase smb-1 bound to L-captopril”. X-ray diffraction, 4 ligands (X8Z, ZN, NA), 1 pocket (best druggability 0.43). MolNFT v1 #113974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AYA
Type: protein
Length: 259 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase
EC: 3.5.2.6
UniProt: G5ELM3
Ligands: X8Z, ZN, NA, SO4
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallo-beta-lactamase (EC 3.5.2.6)	protein	259	36% helix, 23% strand	G5ELM3

Ligands and binding sites

X8Z · L-captopril · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
NA · Sodium ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.43	0.79	23	X8Z

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5AYA · Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to L-captopril · 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 G5ELM3
Elsewhere: RCSB PDB 5AYA · PDBe 5AYA · UniProt G5ELM3

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