Research workbench
Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp or dthd
Analyse Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp or dthd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUW
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymdine kinase
- EC
- 2.7.1.21
- UniProt
- Q38CF2
- Ligands
- QBT, THM, ZN, PO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymdine kinase (EC 2.7.1.21) | protein | 168 | 32% helix, 26% strand | Q38CF2 |
| B | Thymdine kinase (EC 2.7.1.21) | protein | 166 | 32% helix, 26% 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 · chains A
- THM · Thymidine · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 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 | 179 | 0.57 | 0.80 | 36 | QBT, PO4 |
| 2 | 141 | 0.55 | 0.81 | 27 | PO4, THM |
| 3 | 79 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1129 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FUW · catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd · 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 5FUW · PDBe 5FUW · UniProt Q38CF2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.