Research workbench
Crystal structure of ATP bound thymidylate kinase from thermus thermophilus HB8
Analyse Crystal structure of ATP bound thymidylate kinase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X8A
- Type
- protein
- Length
- 386 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q5SHX3
- Ligands
- ATP, MG, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 197 | 51% helix, 14% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 189 | 55% helix, 14% strand | Q5SHX3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.69 | 0.79 | 41 | MG |
| 2 | 52 | 0.39 | 0.81 | 16 | empty |
| 3 | 65 | 0.34 | 0.77 | 11 | empty |
| 4 | 54 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5X8A · Crystal structure of ATP bound thymidylate kinase from thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHX3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q5SHX3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q5SHX3
- Elsewhere: RCSB PDB 5X8A · PDBe 5X8A · UniProt Q5SHX3
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