MolNFT v1 · #76238 · protein
S74E-dck mutant in complex with udp
3QEJ · Deoxycytidine kinase: “S74E-dck mutant in complex with udp”. X-ray diffraction, 1 ligand (UDP), 3 pockets (best druggability 0.73). MolNFT v1 #76238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3QEJ
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine kinase
- EC
- 2.7.1.74
- UniProt
- P27707
- Ligands
- UDP
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 234 | 59% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 234 | 58% helix, 11% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.73 | 0.84 | 42 | UDP |
| 2 | 348 | 0.73 | 0.85 | 39 | empty |
| 3 | 78 | 0.38 | 0.77 | 12 | UDP |
Interfaces
1 interface between chains.
- A–B · 1309 Ų buried · 13 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 3QEJ · PDBe 3QEJ · UniProt P27707
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