MolNFT v1 · #108132 · protein
Leishmania major thymidine kinase in complex with thymidine
4UXI: “Leishmania major thymidine kinase in complex with thymidine”. X-ray diffraction, 3 ligands (THM, ZN, PO4), 3 pockets (best druggability 0.53). MolNFT v1 #108132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UXI
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- Q4QC75
- Ligands
- THM, ZN, PO4
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 164 | 29% helix, 28% strand | Q4QC75 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 160 | 29% helix, 28% strand | Q4QC75 |
Ligands and binding sites
- THM · Thymidine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.53 | 0.81 | 24 | PO4, THM |
| 2 | 87 | 0.48 | 0.82 | 24 | PO4, THM |
| 3 | 52 | 0.30 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4UXI · Leishmania major Thymidine Kinase in complex with thymidine · 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 Q4QC75
- Elsewhere: RCSB PDB 4UXI · PDBe 4UXI · UniProt Q4QC75
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