Research workbench
Dephospho-CoA kinase from campylobacter jejuni.
Analyse Dephospho-CoA kinase from campylobacter jejuni. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZO4
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dephospho-CoA kinase
- EC
- 2.7.1.24
- UniProt
- Q9PMD9
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 202 | 58% helix, 13% strand | Q9PMD9 |
| B, D | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 194 | 58% helix, 14% strand | Q9PMD9 |
| C | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 201 | 58% helix, 15% strand | Q9PMD9 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.81 | 0.90 | 68 | empty |
| 2 | 427 | 0.79 | 0.87 | 64 | empty |
| 3 | 442 | 0.77 | 0.86 | 56 | empty |
| 4 | 458 | 0.76 | 0.85 | 64 | empty |
| 5 | 312 | 0.69 | 0.82 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2043 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1987 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 691 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 468 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 1 covalent (engineered, additive adduct).
Compared structures
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 Q9PMD9
- Elsewhere: RCSB PDB 4ZO4 · PDBe 4ZO4 · UniProt Q9PMD9
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