MolNFT v1 · #56531 · protein
C4S dck variant of dck in complex with L-DA+UDP
2ZI5 · Deoxycytidine kinase: “C4S dck variant of dck in complex with L-DA+UDP”. X-ray diffraction, 2 ligands (UDP, 3L1), 7 pockets (best druggability 0.79). MolNFT v1 #56531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZI5
- Type
- protein
- Length
- 879 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, 3L1
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 219 | 55% helix, 12% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 223 | 59% helix, 12% strand | P27707 |
| C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 219 | 56% helix, 12% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 218 | 58% helix, 12% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 3L1 · (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.79 | 0.80 | 100 | UDP, 3L1 |
| 2 | 366 | 0.72 | 0.83 | 47 | UDP, 3L1 |
| 3 | 316 | 0.72 | 0.84 | 41 | UDP, 3L1 |
| 4 | 367 | 0.72 | 0.83 | 46 | UDP, 3L1 |
| 5 | 129 | 0.51 | 0.80 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1172 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 397 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 275 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 6 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 2ZI5 · PDBe 2ZI5 · UniProt P27707
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.