MolNFT v1 · #22379 · protein
X-ray structure of dephospho-CoA kinase from E. COLI norteast structural genomics consortium target ER57
1T3H: “X-ray structure of dephospho-CoA kinase from E. COLI norteast structural genomics consortium target ER57”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.70). MolNFT v1 #22379 on GenesisL1: 3D structure, binding…
- PDB
- 1T3H
- Type
- protein
- Length
- 601 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
- SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 207 | 52% helix, 13% strand | P0A6I9 |
| C | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 187 | 49% helix, 13% strand | P0A6I9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.70 | 0.77 | 62 | empty |
| 2 | 450 | 0.62 | 0.76 | 34 | empty |
| 3 | 434 | 0.60 | 0.75 | 37 | empty |
| 4 | 193 | 0.51 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- B–C · 285 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1T3H · X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics… · 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 0.93
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 1T3H · PDBe 1T3H · UniProt P0A6I9
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