Research workbench
Crystal structure of the putative dephospho-CoA kinase from aquifex aeolicus, northeast structural genomics target QR72.
Analyse Crystal structure of the putative dephospho-CoA kinase from aquifex aeolicus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IF2
- Type
- protein
- Length
- 551 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
- O67792
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 194 | 51% helix, 13% strand | O67792 |
| C | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 163 | 47% helix, 15% strand | O67792 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 65 | SO4, EDO |
| 2 | 375 | 0.72 | 0.84 | 50 | SO4 |
| 3 | 543 | 0.68 | 0.78 | 44 | SO4 |
| 4 | 294 | 0.58 | 0.78 | 37 | empty |
| 5 | 211 | 0.57 | 0.79 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–C · 803 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2IF2 · Crystal Structure of the Putative Dephospho-CoA Kinase from Aquifex aeolicus, Northeast… · the same entry in another collection · chain A against A, TM-score 1.00
- O67792 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (O67792) · a predicted model of the same protein · chain B 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 O67792
- Elsewhere: RCSB PDB 2IF2 · PDBe 2IF2 · UniProt O67792
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