Research workbench
Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine monophosphate
Analyse Crystal structure of human uridine-cytidine kinase 2 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N54
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine-cytidine kinase 2
- EC
- 2.7.1.48
- UniProt
- Q9BZX2
- Ligands
- KEA, MG, PO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 210 | 50% helix, 21% strand | Q9BZX2 |
| B | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 213 | 49% helix, 21% strand | Q9BZX2 |
Ligands and binding sites
- KEA · 2'-azido-2'-deoxycytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.70 | 0.83 | 40 | MG, PO4, KEA |
| 2 | 331 | 0.64 | 0.80 | 38 | MG, PO4, KEA |
| 3 | 157 | 0.60 | 0.83 | 28 | GOL |
| 4 | 189 | 0.46 | 0.74 | 23 | empty |
| 5 | 156 | 0.44 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6N54 · Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BZX2 · AlphaFold monomer V2.0 prediction for uridine-cytidine kinase 2 (Q9BZX2) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9BZX2
- Elsewhere: RCSB PDB 6N54 · PDBe 6N54 · UniProt Q9BZX2
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