Research workbench
Crystal structure of cmp kinase in complex with cdp and ADP from thermus thermophilus HB8
Analyse Crystal structure of cmp kinase in complex with cdp and ADP from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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