Research workbench
C4S dck variant of dck in complex with D-DG+UDP
Analyse C4S dck variant of dck in complex with D-DG+UDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZI7
- Type
- protein
- Length
- 426 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
- GNG, UDP
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 208 | 56% helix, 13% strand | P27707 |
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 218 | 58% helix, 12% strand | P27707 |
Ligands and binding sites
- GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains B, A
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.66 | 0.86 | 31 | GNG, UDP |
| 2 | 163 | 0.66 | 0.86 | 31 | GNG, UDP |
| 3 | 60 | 0.33 | 0.76 | 18 | empty |
| 4 | 52 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1306 Ų buried · 10 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 2ZI7 · PDBe 2ZI7 · UniProt P27707
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