Research workbench
Crystal structure of thymidylate kinase in complex with dtdp and ADP from thermotoga maritima
Analyse Crystal structure of thymidylate kinase in complex with dtdp and ADP from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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