MolNFT v1 · #66209 · protein
Crystal structure of thymidylate kinase in complex with dtdp and ADP from thermotoga maritima
3HJN: “Crystal structure of thymidylate kinase in complex with dtdp and ADP from thermotoga maritima”. X-ray diffraction, 3 ligands (ADP, TYD, MG), 5 pockets (best druggability 0.60). MolNFT v1 #66209 on GenesisL1: 3D structure, binding…
- PDB
- 3HJN
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9X0I3
- Ligands
- ADP, TYD, MG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 189 | 57% helix, 14% strand | Q9X0I3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 184 | 52% helix, 14% strand | Q9X0I3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.60 | 0.83 | 28 | ADP, TYD, MG |
| 2 | 144 | 0.58 | 0.83 | 26 | TYD |
| 3 | 84 | 0.47 | 0.82 | 15 | empty |
| 4 | 61 | 0.43 | 0.82 | 14 | empty |
| 5 | 54 | 0.27 | 0.73 | 8 | empty |
Interfaces
1 interface between chains.
- A–B · 1068 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3HJN · Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9X0I3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9X0I3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9X0I3
- Elsewhere: RCSB PDB 3HJN · PDBe 3HJN · UniProt Q9X0I3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.