Research workbench
Crystal structure of dephosphocoenzyme a kinase from escherichia COLI
Analyse Crystal structure of dephosphocoenzyme a kinase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N3B
- Type
- protein
- Length
- 588 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
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 176 | 56% helix, 14% strand | P0A6I9 |
| B, C | Dephospho-CoA kinase (EC 2.7.1.24) | protein | 206 | 56% helix, 13% strand | P0A6I9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.77 | 0.80 | 101 | SO4 |
| 2 | 553 | 0.73 | 0.81 | 52 | SO4 |
| 3 | 327 | 0.67 | 0.82 | 41 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 820 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 800 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1N3B · Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli · 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 A against A, TM-score 0.95
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 1N3B · PDBe 1N3B · UniProt P0A6I9
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