MolNFT v1 · #119248 · protein
Crystal structure of the OXA10 with 1C
5FQ9 · Beta-lactamase oxa-10: “Crystal structure of the OXA10 with 1C”. X-ray diffraction, 3 ligands (C6S, NA, CL), 4 pockets (best druggability 0.71). MolNFT v1 #119248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FQ9
- 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
- C6S, NA, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 246 | 40% helix, 25% strand | P14489 |
| B | Beta-lactamase oxa-10 (EC 3.5.2.6) | protein | 247 | 39% helix, 25% strand | P14489 |
Ligands and binding sites
- C6S · (3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.71 | 0.94 | 29 | ACT |
| 2 | 90 | 0.64 | 0.90 | 25 | empty |
| 3 | 207 | 0.47 | 0.75 | 31 | C6S |
| 4 | 100 | 0.38 | 0.75 | 20 | C6S |
Interfaces
1 interface between chains.
- A–B · 1318 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, carboxylation).
Compared structures
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 5FQ9 · PDBe 5FQ9 · UniProt P14489
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