MolNFT v1 · #30571 · protein
Crystal structure of human deoxycytidine kinase in complex with deoxycytidine
2A30: “Crystal structure of human deoxycytidine kinase in complex with deoxycytidine”. X-ray diffraction, 2 ligands (DCZ, CA), 9 pockets (best druggability 0.72). MolNFT v1 #30571 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2A30
- Type
- protein
- Length
- 869 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, CA
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 221 | 55% helix, 12% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 212 | 57% helix, 12% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 215 | 57% helix, 13% strand | P27707 |
Ligands and binding sites
- DCZ · 2'-deoxycytidine · ligand · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.72 | 0.92 | 29 | DCZ |
| 2 | 119 | 0.68 | 0.90 | 26 | DCZ |
| 3 | 145 | 0.64 | 0.86 | 26 | DCZ |
| 4 | 124 | 0.64 | 0.87 | 22 | DCZ |
| 5 | 128 | 0.51 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1313 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2A30 · Crystal structure of human deoxycytidine kinase in complex with deoxycytidine · 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 C 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 2A30 · PDBe 2A30 · UniProt P27707
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