MolNFT v1 · #127232 · protein
Crystal structure of dck mutant C3S
5MQJ · Deoxycytidine kinase: “Crystal structure of dck mutant C3S”. X-ray diffraction, 3 ligands (UDP, UMP, MG), 11 pockets (best druggability 0.70). MolNFT v1 #127232 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MQJ
- Type
- protein
- Length
- 919 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
- UDP, UMP, MG
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 232 | 56% helix, 12% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 228 | 49% helix, 12% strand | P27707 |
| C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 56% helix, 11% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 229 | 53% helix, 11% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.70 | 0.94 | 22 | UMP, MG |
| 2 | 168 | 0.68 | 0.87 | 31 | UDP, UMP, MG |
| 3 | 176 | 0.68 | 0.87 | 31 | UDP, UMP, MG |
| 4 | 140 | 0.64 | 0.87 | 31 | UDP, UMP, MG |
| 5 | 155 | 0.40 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1338 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1247 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 5MQJ · PDBe 5MQJ · UniProt P27707
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