MolNFT v1 · #119399 · protein
Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp
5FUY · Thymdine kinase: “Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp”. X-ray diffraction, 3 ligands (QBT, ZN, PO4), 8 pockets (best druggability 0.78). MolNFT v1 #119399 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FUY
- Type
- protein
- Length
- 988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymdine kinase
- EC
- 2.7.1.21
- UniProt
- Q38CF2
- Ligands
- QBT, ZN, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymdine kinase (EC 2.7.1.21) | protein | 165 | 32% helix, 27% strand | Q38CF2 |
| B | Thymdine kinase (EC 2.7.1.21) | protein | 164 | 32% helix, 25% strand | Q38CF2 |
| C | Thymdine kinase (EC 2.7.1.21) | protein | 164 | 32% helix, 27% strand | Q38CF2 |
| D | Thymdine kinase (EC 2.7.1.21) | protein | 161 | 32% helix, 26% strand | Q38CF2 |
| E | Thymdine kinase (EC 2.7.1.21) | protein | 167 | 32% helix, 27% strand | Q38CF2 |
| F | Thymdine kinase (EC 2.7.1.21) | protein | 167 | 29% helix, 25% strand | Q38CF2 |
Ligands and binding sites
- QBT · [(2R,3S,5R)-3-hydroxy-5-[(5S)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl dihydrogen phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.78 | 0.82 | 75 | empty |
| 2 | 267 | 0.61 | 0.80 | 36 | PO4, QBT |
| 3 | 178 | 0.59 | 0.82 | 30 | PO4, QBT |
| 4 | 172 | 0.57 | 0.81 | 30 | PO4, QBT |
| 5 | 194 | 0.56 | 0.79 | 33 | PO4, QBT |
Interfaces
5 interfaces between chains.
- E–F · 1072 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 972 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 878 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FUY · catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38CF2
- Elsewhere: RCSB PDB 5FUY · PDBe 5FUY · UniProt Q38CF2
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