Research workbench
Cytidine monophosphate kinase from E. COLI in complex with 2'-deoxy-cytidine monophosphate
Analyse Cytidine monophosphate kinase from E. COLI in complex with 2'-deoxy-cytidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KDP
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.14
- UniProt
- P0A6I0
- Ligands
- C, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytidylate kinase (EC 2.7.4.14) | protein | 223 | 51% helix, 14% strand | P0A6I0 |
Ligands and binding sites
- C · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.73 | 0.80 | 62 | SO4, C |
| 2 | 556 | 0.72 | 0.81 | 56 | SO4, C |
| 3 | 69 | 0.34 | 0.76 | 17 | empty |
| 4 | 64 | 0.33 | 0.76 | 14 | empty |
Compared structures
- 1KDP · Cytidine monophosphate kinase from E. COLI in complex with 2'-deoxy-cytidine monophosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6I0 · AlphaFold monomer V2.0 prediction for cytidylate kinase (P0A6I0) · a predicted model of the same protein · chain A 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 P0A6I0
- Elsewhere: RCSB PDB 1KDP · PDBe 1KDP · UniProt P0A6I0
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