MolNFT v1 · #12338 · protein
Cytidine monophosphate kinase from E.COLI in complex with ara-cytidine monophosphate
1KDR · Cytidylate kinase: “Cytidine monophosphate kinase from E.COLI in complex with ara-cytidine monophosphate”. X-ray diffraction, 2 ligands (CAR, SO4), 3 pockets (best druggability 0.74). MolNFT v1 #12338 on GenesisL1: 3D structure…
- PDB
- 1KDR
- Type
- protein
- Length
- 442 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
- CAR, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytidylate kinase (EC 2.7.4.14) | protein | 221 | 48% helix, 14% strand | P0A6I0 |
Ligands and binding sites
- CAR · Cytosine arabinose-5'-phosphate · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.74 | 0.80 | 59 | SO4, CAR |
| 2 | 626 | 0.72 | 0.79 | 66 | SO4, CAR |
| 3 | 77 | 0.32 | 0.74 | 14 | empty |
Compared structures
- 1KDR · Cytidine monophosphate kinase from E.COLI in complex with ara-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 0.97
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 1KDR · PDBe 1KDR · UniProt P0A6I0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.