MolNFT v1 · #106551 · protein
Oxa-48 in complex with avibactam at pH 8.5
4S2N · Beta-lactamase: “Oxa-48 in complex with avibactam at pH 8.5”. X-ray diffraction, 1 ligand (NXL), 5 pockets (best druggability 0.77). MolNFT v1 #106551 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4S2N
- Type
- protein
- Length
- 969 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
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 41% helix, 20% strand | Q6XEC0 |
| B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.77 | 0.80 | 121 | NXL |
| 2 | 813 | 0.76 | 0.80 | 122 | NXL |
| 3 | 161 | 0.45 | 0.76 | 33 | empty |
| 4 | 92 | 0.36 | 0.75 | 23 | empty |
| 5 | 51 | 0.35 | 0.79 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1052 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1047 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 4S2N · OXA-48 in complex with Avibactam at pH 8.5 · the same entry in another collection · chain B against B, 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 4S2N · PDBe 4S2N · UniProt Q6XEC0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.