MolNFT v1 · #25168 · protein
Crystal structure of dephospho-CoA kinase with adenosine-5'- diphosphate
1VHL: “Crystal structure of dephospho-CoA kinase with adenosine-5'- diphosphate”. X-ray diffraction, 1 ligand (ADP), 5 pockets (best druggability 0.70). MolNFT v1 #25168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VHL
- Type
- protein
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dephospho-CoA kinase
- EC
- 2.7.1.24
- UniProt
- P0A6I9
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 208 | 57% helix, 13% strand | P0A6I9 |
| C | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 183 | 47% helix, 13% strand | P0A6I9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains B, C
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 | 801 | 0.70 | 0.76 | 60 | empty |
| 2 | 401 | 0.59 | 0.75 | 36 | empty |
| 3 | 140 | 0.47 | 0.77 | 19 | empty |
| 4 | 115 | 0.46 | 0.78 | 18 | empty |
| 5 | 123 | 0.40 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- B–C · 275 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1VHL · Crystal structure of dephospho-CoA kinase with adenosine-5'-diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6I9 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (P0A6I9) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P0A6I9
- Elsewhere: RCSB PDB 1VHL · PDBe 1VHL · UniProt P0A6I9
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