MolNFT v1 · #131646 · protein

Oxa-48 in complex with compound 23A

5QAR · Beta-lactamase: “Oxa-48 in complex with compound 23A”. X-ray diffraction, 2 ligands (QIU, CL), 11 pockets (best druggability 0.76). MolNFT v1 #131646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QAR
Type: protein
Length: 968 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6XEC0
Ligands: QIU, CL
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-lactamase (EC 3.5.2.6)	protein	242	40% helix, 20% strand	Q6XEC0

Ligands and binding sites

QIU · 3-[3-(2-acetamidoethyl)phenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · chains B

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

Pockets

11 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	672	0.76	0.81	88	QIU
2	501	0.73	0.82	61	empty
3	353	0.64	0.79	41	empty
4	189	0.48	0.76	27	empty
5	120	0.39	0.74	22	QIU

Interfaces

4 interfaces between chains.

A–B · 467 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 361 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 269 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 258 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

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 5QAR · PDBe 5QAR · UniProt Q6XEC0

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