Research workbench
Oxa-48 covalent complex with avibactam inhibitor
Analyse Oxa-48 covalent complex with avibactam inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 984 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 967 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 251 Ų 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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