Research workbench
Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp
Analyse Catalytic domain of thymidine kinase from trypanosoma brucei with dtmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUX
- Type
- protein
- Length
- 333 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, ZN, MG, PO4
- Pockets
- 2 · 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 | 31% helix, 26% strand | Q38CF2 |
| B | Thymdine kinase (EC 2.7.1.21) | protein | 165 | 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 · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.57 | 0.81 | 35 | MG, PO4, QBT |
| 2 | 143 | 0.55 | 0.81 | 26 | PO4, QBT |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FUX · 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 5FUX · PDBe 5FUX · UniProt Q38CF2
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