Research workbench
Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine
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
- 6PWZ
- Type
- protein
- Length
- 1,696 residues
- Chains
- 8
- 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
- P6D, PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 213 | 48% helix, 15% strand | Q9BZX2 |
| B | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 215 | 46% helix, 20% strand | Q9BZX2 |
| C | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 212 | 48% helix, 18% strand | Q9BZX2 |
| D | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 212 | 49% helix, 18% strand | Q9BZX2 |
| E | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 213 | 49% helix, 21% strand | Q9BZX2 |
| F, G | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 213 | 48% helix, 20% strand | Q9BZX2 |
| H | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 205 | 48% helix, 17% strand | Q9BZX2 |
Ligands and binding sites
- P6D · 2'-azidocytidine · ligand · 3 copies · chains D, E, H
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 30 copies · chains A, D, G, B, H, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.74 | 0.77 | 89 | GOL |
| 2 | 437 | 0.65 | 0.78 | 50 | PO4 |
| 3 | 98 | 0.64 | 0.89 | 20 | GOL |
| 4 | 225 | 0.62 | 0.82 | 48 | GOL |
| 5 | 227 | 0.61 | 0.81 | 45 | GOL |
Interfaces
15 interfaces between chains.
- B–H · 871 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 815 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 799 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 789 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 686 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PWZ · Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine · the same entry in another collection · chain H against H, TM-score 1.00
- Q9BZX2 · AlphaFold monomer V2.0 prediction for uridine-cytidine kinase 2 (Q9BZX2) · a predicted model of the same protein · chain H 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 6PWZ · PDBe 6PWZ · UniProt Q9BZX2
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