MolNFT v1 · #30570 · protein
Crystal structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate
2A2Z: “Crystal structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate”. X-ray diffraction, 4 ligands (DCZ, UDP, MG), 8 pockets (best druggability 0.72). MolNFT v1 #30570 on GenesisL1: 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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