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Crystal structure of a dephospho-CoA kinase from burkholderia vietnamiensis bound to ADP
Analyse Crystal structure of a dephospho-CoA kinase from burkholderia vietnamiensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I1V
- Type
- protein
- Length
- 409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dephospho-CoA kinase
- EC
- 2.7.1.24
- UniProt
- A4JBA9
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 207 | 55% helix, 12% strand | A4JBA9 |
| B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 202 | 56% helix, 12% strand | A4JBA9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.72 | 0.80 | 67 | ADP |
| 2 | 459 | 0.70 | 0.80 | 39 | empty |
| 3 | 164 | 0.70 | 0.89 | 33 | empty |
| 4 | 150 | 0.49 | 0.78 | 29 | empty |
| 5 | 58 | 0.31 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4I1V · Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP · 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 A4JBA9
- Elsewhere: RCSB PDB 4I1V · PDBe 4I1V · UniProt A4JBA9
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