MolNFT v1 · #108924 · protein

Oxa-48 covalent complex with avibactam inhibitor

4WMC · Beta-lactamase: “Oxa-48 covalent complex with avibactam inhibitor”. X-ray diffraction, 2 ligands (NXL, CO2), 13 pockets (best druggability 0.79). MolNFT v1 #108924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WMC
Type: protein
Length: 1,873 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q6XEC0
Ligands: NXL, CO2
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	237	40% helix, 21% strand	Q6XEC0
B	Beta-lactamase (EC 3.5.2.6)	protein	235	43% helix, 22% strand	Q6XEC0
C	Beta-lactamase (EC 3.5.2.6)	protein	230	44% helix, 21% strand	Q6XEC0
D	Beta-lactamase (EC 3.5.2.6)	protein	236	39% helix, 22% strand	Q6XEC0
E	Beta-lactamase (EC 3.5.2.6)	protein	239	41% helix, 19% strand	Q6XEC0
F	Beta-lactamase (EC 3.5.2.6)	protein	240	39% helix, 21% strand	Q6XEC0
G	Beta-lactamase (EC 3.5.2.6)	protein	235	43% helix, 21% strand	Q6XEC0
H	Beta-lactamase (EC 3.5.2.6)	protein	221	42% helix, 23% strand	Q6XEC0

Ligands and binding sites

NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CO2 · Carbon dioxide · ion · 3 copies · chains A, C, F

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.79	0.82	117	empty
2	941	0.77	0.80	126	NXL
3	669	0.77	0.82	98	NXL
4	746	0.76	0.81	107	NXL
5	77	0.43	0.80	17	empty

Interfaces

8 interfaces between chains.

D–E · 1024 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 987 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 984 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 967 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 251 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent, 2 modified (covalent ligand, carboxylation).

Compared structures

4WMC · OXA-48 covalent complex with Avibactam inhibitor · 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 4WMC · PDBe 4WMC · UniProt Q6XEC0

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