MolNFT v1 · #71624 · protein
Human dck complex with acyclic nucleoside
3MJR · Deoxycytidine kinase: “Human dck complex with acyclic nucleoside”. X-ray diffraction, 2 ligands (UDP, AC2), 12 pockets (best druggability 0.76). MolNFT v1 #71624 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MJR
- Type
- protein
- Length
- 899 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, AC2
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine kinase (EC 2.7.1.74) | protein | 230 | 51% helix, 11% strand | P27707 |
| B | Deoxycytidine kinase (EC 2.7.1.74) | protein | 226 | 54% helix, 12% strand | P27707 |
| C | Deoxycytidine kinase (EC 2.7.1.74) | protein | 222 | 44% helix, 9% strand | P27707 |
| D | Deoxycytidine kinase (EC 2.7.1.74) | protein | 221 | 44% helix, 11% strand | P27707 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- AC2 · 9-hyroxyethoxymethylguanine · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.76 | 0.83 | 55 | UDP |
| 2 | 650 | 0.76 | 0.81 | 52 | AC2, UDP |
| 3 | 443 | 0.74 | 0.83 | 47 | AC2, UDP |
| 4 | 481 | 0.71 | 0.81 | 50 | AC2, UDP |
| 5 | 90 | 0.69 | 0.93 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1155 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 961 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 3MJR · PDBe 3MJR · UniProt P27707
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