MolNFT v1 · #108133 · protein
Leishmania major thymidine kinase in complex with dttp
4UXJ: “Leishmania major thymidine kinase in complex with dttp”. X-ray diffraction, 3 ligands (TTP, ZN, MG), 16 pockets (best druggability 0.66). MolNFT v1 #108133 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UXJ
- Type
- protein
- Length
- 1,332 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- Q4QC75
- Ligands
- TTP, ZN, MG
- Pockets
- 16 · best druggability 0.66
Structure
x-ray diffraction · 8 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 167 | 28% helix, 28% strand | Q4QC75 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 166 | 28% helix, 27% strand | Q4QC75 |
| C | Thymidine kinase (EC 2.7.1.21) | protein | 171 | 27% helix, 29% strand | Q4QC75 |
| D | Thymidine kinase (EC 2.7.1.21) | protein | 159 | 29% helix, 28% strand | Q4QC75 |
| E | Thymidine kinase (EC 2.7.1.21) | protein | 170 | 28% helix, 25% strand | Q4QC75 |
| F | Thymidine kinase (EC 2.7.1.21) | protein | 173 | 27% helix, 26% strand | Q4QC75 |
| G | Thymidine kinase (EC 2.7.1.21) | protein | 169 | 27% helix, 30% strand | Q4QC75 |
| H | Thymidine kinase (EC 2.7.1.21) | protein | 157 | 27% helix, 28% strand | Q4QC75 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.66 | 0.82 | 51 | empty |
| 2 | 268 | 0.62 | 0.80 | 40 | TTP, MG |
| 3 | 180 | 0.59 | 0.82 | 33 | TTP, MG |
| 4 | 184 | 0.58 | 0.81 | 33 | TTP |
| 5 | 140 | 0.56 | 0.83 | 31 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1133 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1066 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1042 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 901 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4UXJ · Leishmania major Thymidine Kinase in complex with dTTP · 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 4UXJ · PDBe 4UXJ · UniProt Q4QC75
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.