Research workbench
Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidouridine
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
- 6N55
- Type
- protein
- Length
- 1,670 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
- UZ0, PO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 201 | 45% helix, 21% strand | Q9BZX2 |
| B | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 206 | 45% helix, 17% 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 | 213 | 47% helix, 21% strand | Q9BZX2 |
| E | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 214 | 48% helix, 18% strand | Q9BZX2 |
| F | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 212 | 49% helix, 21% strand | Q9BZX2 |
| G | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 201 | 46% helix, 17% strand | Q9BZX2 |
| H | Uridine-cytidine kinase 2 (EC 2.7.1.48) | protein | 211 | 44% helix, 20% strand | Q9BZX2 |
Ligands and binding sites
- UZ0 · 2'-azido-2'-deoxyuridine · ligand · 3 copies · chains D, E, F
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 27 copies · chains A, F, C, B, E, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.71 | 0.79 | 47 | PO4 |
| 2 | 517 | 0.70 | 0.80 | 46 | UZ0 |
| 3 | 550 | 0.66 | 0.77 | 60 | PO4 |
| 4 | 257 | 0.61 | 0.80 | 41 | PO4, GOL |
| 5 | 344 | 0.60 | 0.77 | 39 | PO4 |
Interfaces
14 interfaces between chains.
- A–H · 847 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 831 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 788 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 696 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 686 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6N55 · Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidouridine · 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 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 Q9BZX2
- Elsewhere: RCSB PDB 6N55 · PDBe 6N55 · UniProt Q9BZX2
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