MolNFT v1 · #12340 · protein
Cytidine monophosphate kinase from E.COLI in complex with 2',3'-dideoxy-cytidine monophosphate
1KDT · Cytidylate kinase: “Cytidine monophosphate kinase from E.COLI in complex with 2',3'-dideoxy-cytidine monophosphate”. X-ray diffraction, 2 ligands (DOC, SO4), 2 pockets (best druggability 0.75). MolNFT v1 #12340 on GenesisL1: 3D…
- PDB
- 1KDT
- 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
- DOC, SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytidylate kinase (EC 2.7.4.14) | protein | 223 | 50% helix, 15% strand | P0A6I0 |
Ligands and binding sites
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.75 | 0.81 | 72 | SO4, DOC |
| 2 | 612 | 0.71 | 0.79 | 72 | SO4, DOC |
Compared structures
- 1KDT · Cytidine monophosphate kinase from E.COLI in complex with 2',3'-dideoxy-cytidine… · 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 1KDT · PDBe 1KDT · UniProt P0A6I0
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