MolNFT v1 · #179446 · protein

Oxa-48 bound by compound 3.1

7K5V · Beta-lactamase: “Oxa-48 bound by compound 3.1”. X-ray diffraction, 3 ligands (BIH, NA, CL), 2 pockets (best druggability 0.78). MolNFT v1 #179446 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K5V
Type: protein
Length: 484 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6XEC0
Ligands: BIH, NA, CL
Pockets: 2 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	242	42% helix, 20% strand	Q6XEC0

Ligands and binding sites

BIH · Naphthalene-2,6-disulfonic acid · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · chains A, B
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

2 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	855	0.78	0.81	124	BIH, CL, NA
2	56	0.38	0.80	16	empty

Interfaces

1 interface between chains.

A–B · 1034 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

7K5V · OXA-48 bound by Compound 3.1 · 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 Q6XEC0
Elsewhere: RCSB PDB 7K5V · PDBe 7K5V · UniProt Q6XEC0

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