MolNFT v1 · #94610 · protein
Apo crystal structure of a dephospho-CoA kinase from burkholderia vietnamiensis
4I1U: “Apo crystal structure of a dephospho-CoA kinase from burkholderia vietnamiensis”. X-ray diffraction, 2 ligands (SO4, CL), 6 pockets (best druggability 0.76). MolNFT v1 #94610 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4I1U
- Type
- protein
- Length
- 407 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
- SO4, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 205 | 58% helix, 12% strand | A4JBA9 |
| B | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 202 | 59% helix, 12% strand | A4JBA9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.76 | 0.81 | 56 | SO4 |
| 2 | 663 | 0.75 | 0.81 | 44 | SO4 |
| 3 | 55 | 0.66 | 0.95 | 15 | empty |
| 4 | 72 | 0.65 | 0.92 | 16 | empty |
| 5 | 134 | 0.53 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4I1U · Apo crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis · 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 4I1U · PDBe 4I1U · UniProt A4JBA9
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