MolNFT v1 · #106547 · protein
Oxa-48 in complex with avibactam at pH 6.5
4S2J · Beta-lactamase: “Oxa-48 in complex with avibactam at pH 6.5”. X-ray diffraction, 1 ligand (NXL), 7 pockets (best druggability 0.78). MolNFT v1 #106547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4S2J
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- NXL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | Q6XEC0 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.78 | 0.81 | 121 | NXL |
| 2 | 911 | 0.78 | 0.80 | 123 | NXL |
| 3 | 831 | 0.72 | 0.77 | 79 | empty |
| 4 | 61 | 0.39 | 0.80 | 18 | empty |
| 5 | 58 | 0.37 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1005 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 354 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4S2J · OXA-48 in complex with Avibactam at pH 6.5 · 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 4S2J · PDBe 4S2J · UniProt Q6XEC0
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