MolNFT v1 · #57840 · protein
Crystal structure of cmp kinase in complex with cdp and ADP from thermus thermophilus HB8
3AKC · Cytidylate kinase: “Crystal structure of cmp kinase in complex with cdp and ADP from thermus thermophilus HB8”. X-ray diffraction, 3 ligands (CDP, ADP, GD), 1 pocket (best druggability 0.69). MolNFT v1 #57840 on GenesisL1: 3D…
- PDB
- 3AKC
- Type
- protein
- Length
- 208 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidylate kinase
- EC
- 2.7.4.14
- UniProt
- Q5SL35
- Ligands
- CDP, ADP, GD
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytidylate kinase (EC 2.7.4.14) | protein | 208 | 51% helix, 16% strand | Q5SL35 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- GD · Gadolinium atom · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.69 | 0.83 | 44 | CDP, ADP, GD |
Compared structures
- 3AKC · Crystal structure of CMP kinase in complex with CDP and ADP from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SL35 · AlphaFold monomer V2.0 prediction for cytidylate kinase (Q5SL35) · 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 Q5SL35
- Elsewhere: RCSB PDB 3AKC · PDBe 3AKC · UniProt Q5SL35
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