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Toho-1 beta-lactamase in complex with benzylpenicillin

Analyse Toho-1 beta-lactamase in complex with benzylpenicillin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IYQ
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toho-1 beta-lactamase
EC: 3.5.2.6
UniProt: Q47066
Ligands: PNM, SO4
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toho-1 beta-lactamase (EC 3.5.2.6)	protein	261	42% helix, 20% strand	Q47066

Ligands and binding sites

PNM · Open form - penicillin G · ligand · chains A
SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.34	0.77	19	PNM

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1IYQ · Toho-1 beta-Lactamase In Complex With Benzylpenicillin · the same entry in another collection · chain A against A, TM-score 1.00
Q47066 · AlphaFold monomer V2.0 prediction for beta-lactamase toho-1 (Q47066) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q47066
Elsewhere: RCSB PDB 1IYQ · PDBe 1IYQ · UniProt Q47066

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