MolNFT v1 · #174510 · protein
2-amino-3-ketobutyrate CoA ligase from cupriavidus necator 3- hydroxynorvaline binding form
7BXR · 2-amino-3-ketobutyrate coenzyme a ligase: “2-amino-3-ketobutyrate CoA ligase from cupriavidus necator 3- hydroxynorvaline binding form”. X-ray diffraction, 1 ligand (F9X), 10 pockets (best druggability 0.80). MolNFT v1 #174510 on…
- PDB
- 7BXR
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-3-ketobutyrate coenzyme a ligase
- EC
- 2.3.1.29
- UniProt
- Q0K313
- Ligands
- F9X
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-amino-3-ketobutyrate coenzyme a ligase (EC 2.3.1.29) | protein | 399 | 44% helix, 16% strand | Q0K313 |
Ligands and binding sites
- F9X · (2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.80 | 0.97 | 38 | F9X |
| 2 | 154 | 0.80 | 0.96 | 35 | F9X |
| 3 | 60 | 0.72 | 0.98 | 24 | empty |
| 4 | 275 | 0.54 | 0.76 | 43 | empty |
| 5 | 255 | 0.52 | 0.75 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 4794 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 7BXR · 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form · 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 Q0K313
- Elsewhere: RCSB PDB 7BXR · PDBe 7BXR · UniProt Q0K313
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