MolNFT v1 · #38246 · protein
Crystal structure of dephospho-CoA kinase (ec 2.7.1.24) (dephosphocoenzyme a kinase) (TM1387) from thermotoga maritima at 2.60 a resolution
2GRJ: “Crystal structure of dephospho-CoA kinase (ec 2.7.1.24) (dephosphocoenzyme a kinase) (TM1387) from thermotoga…”. X-ray diffraction, 3 ligands (ADP, COD, CL), 12 pockets (best druggability 0.89). MolNFT v1 #38246 on GenesisL1: 3D…
- PDB
- 2GRJ
- Type
- protein
- Length
- 1,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dephospho-CoA kinase
- EC
- 2.7.1.24
- UniProt
- Q9X1A7
- Ligands
- ADP, COD, CL
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 179 | 54% helix, 16% strand | Q9X1A7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- COD · Dephospho coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.89 | 0.90 | 104 | ADP, COD |
| 2 | 1067 | 0.89 | 0.90 | 118 | ADP, COD |
| 3 | 763 | 0.87 | 0.90 | 95 | ADP, COD |
| 4 | 460 | 0.83 | 0.90 | 53 | ADP, COD |
| 5 | 450 | 0.83 | 0.90 | 52 | ADP, COD |
Interfaces
13 interfaces between chains.
- G–H · 872 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 803 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 743 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 700 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 419 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2GRJ · Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase)… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9X1A7 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (Q9X1A7) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 Q9X1A7
- Elsewhere: RCSB PDB 2GRJ · PDBe 2GRJ · UniProt Q9X1A7
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