Research workbench
Crystal structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate
Analyse Crystal structure of human deoxycytidine kinase in complex with deoxycytidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A2Z
- Type
- protein
- Length
- 885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine kinase
- EC
- 2.7.1.74
- UniProt
- P27707
- Ligands
- DCZ, UDP, MG, CA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 222 | 54% helix, 12% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 221 | 52% helix, 12% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 220 | 52% helix, 12% strand | P27707 |
Ligands and binding sites
- DCZ · 2'-deoxycytidine · ligand · 4 copies · chains A, B, C, D
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.72 | 0.93 | 23 | MG, DCZ |
| 2 | 100 | 0.70 | 0.93 | 23 | MG, DCZ |
| 3 | 95 | 0.67 | 0.91 | 22 | MG, DCZ |
| 4 | 174 | 0.67 | 0.86 | 32 | MG, DCZ, UDP |
| 5 | 73 | 0.36 | 0.77 | 13 | UDP |
Interfaces
3 interfaces between chains.
- A–B · 1272 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1261 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2A2Z · Crystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine… · the same entry in another collection · chain D against D, TM-score 1.00
- P27707 · AlphaFold monomer V2.0 prediction for deoxycytidine kinase (P27707) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P27707
- Elsewhere: RCSB PDB 2A2Z · PDBe 2A2Z · UniProt P27707
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