MolNFT v1 · #109560 · protein

Crystal structure of OP0595 complexed with ctx-M-44

4X69 · Beta-lactamase toho-1: “Crystal structure of OP0595 complexed with ctx-M-44”. X-ray diffraction, 1 ligand (OP0), 3 pockets (best druggability 0.66). MolNFT v1 #109560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X69
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase toho-1
EC: 3.5.2.6
UniProt: Q47066
Ligands: OP0
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase toho-1 (EC 3.5.2.6)	protein	261	43% helix, 20% strand	Q47066

Ligands and binding sites

OP0 · (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy) amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 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	721	0.66	0.75	73	OP0
2	93	0.38	0.76	20	OP0
3	52	0.35	0.79	18	EDO

Interfaces

1 interface between chains.

A–B · 293 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4X69 · Crystal structure of OP0595 complexed with CTX-M-44 · 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 B 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 Q47066
Elsewhere: RCSB PDB 4X69 · PDBe 4X69 · UniProt Q47066

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