MolNFT v1 · #127144 · protein

Oxa-10 avibactam complex with bound bromide

5MNU · Beta-lactamase oxa-10: “Oxa-10 avibactam complex with bound bromide”. X-ray diffraction, 3 ligands (NXL, NA, BR), 4 pockets (best druggability 0.75). MolNFT v1 #127144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MNU
Type: protein
Length: 493 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, BR
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	246	39% helix, 25% strand	P14489
B	Beta-lactamase oxa-10 (EC 3.5.2.6)	protein	247	38% helix, 26% 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 · chains A
BR · Bromide ion · ion · 6 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B

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

Pockets

4 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	141	0.75	0.93	32	GOL
2	123	0.71	0.92	24	empty
3	203	0.51	0.77	42	NXL, BR
4	174	0.44	0.74	37	NXL

Interfaces

1 interface between chains.

A–B · 1379 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5MNU · OXA-10 Avibactam complex with bound bromide · 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 5MNU · PDBe 5MNU · UniProt P14489

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