MolNFT v1 · #127185 · protein

Oxa-10 avibactam complex with bound iodide

5MOZ · Beta-lactamase oxa-10: “Oxa-10 avibactam complex with bound iodide”. X-ray diffraction, 4 ligands (NXL, NA, IOD), 5 pockets (best druggability 0.76). MolNFT v1 #127185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MOZ
Type: protein
Length: 494 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, NA, IOD, CL
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	247	39% 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
NA · Sodium ion · metal · 6 copies · chains A, B
IOD · Iodide ion · ion · 8 copies · chains A, B
CL · Chloride ion · ion · chains B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

5 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	143	0.76	0.94	31	GOL
2	152	0.74	0.92	34	GOL
3	226	0.51	0.75	36	NXL, GOL, IOD
4	93	0.40	0.77	23	IOD, NXL
5	86	0.37	0.76	22	empty

Interfaces

1 interface between chains.

A–B · 1388 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5MOZ · OXA-10 Avibactam complex with bound Iodide · 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 B 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 5MOZ · PDBe 5MOZ · UniProt P14489

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