Research workbench
Crystal structure of a dephospho-CoA kinase from escherichia COLI in complex with inhibitor CM078
Analyse Crystal structure of a dephospho-CoA kinase from escherichia COLI in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ARI
- Type
- protein
- Length
- 403 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
- P0A6I9
- Ligands
- BQV
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 200 | 58% helix, 14% strand | P0A6I9 |
| B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 203 | 60% helix, 14% strand | P0A6I9 |
Ligands and binding sites
- BQV · N-(methylsulfonyl)-3-{[(thiophen-2-yl) sulfanyl]methyl}benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.53 | 0.84 | 19 | empty |
| 2 | 276 | 0.53 | 0.75 | 26 | BQV |
| 3 | 147 | 0.44 | 0.75 | 21 | BQV |
| 4 | 85 | 0.38 | 0.77 | 20 | empty |
| 5 | 59 | 0.28 | 0.74 | 12 | CIT |
Interfaces
1 interface between chains.
- A–B · 426 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ARI · Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P0A6I9 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (P0A6I9) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 6ARI · PDBe 6ARI · UniProt P0A6I9
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