Research workbench

Oxa-10 in complex with avibactam

Analyse Oxa-10 in complex with avibactam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S2O
Type: protein
Length: 491 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase oxa-10
EC: 3.5.2.6
UniProt: P14489
Ligands: NXL, CO
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	245	40% helix, 23% strand	P14489
B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	246	38% helix, 24% strand	P14489

Ligands and binding sites

NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
CO · Cobalt (II) ion · metal · 4 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.74	0.92	32	empty
2	214	0.71	0.88	32	empty
3	185	0.49	0.76	34	NXL
4	85	0.36	0.75	17	empty
5	64	0.35	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 1260 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4S2O · OXA-10 in complex with Avibactam · the same entry in another collection · chain A against A, TM-score 1.00
P14489 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-10 (P14489) · 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 P14489
Elsewhere: RCSB PDB 4S2O · PDBe 4S2O · UniProt P14489

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