Research workbench
Magnesium bound apo structure of thymidylate kinase (form I) from thermus thermophilus HB8
Analyse Magnesium bound apo structure of thymidylate kinase (form I) from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XT8
- 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
- MG, CL
- Pockets
- 3 · best druggability 0.60
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 | 52% helix, 14% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 189 | 54% helix, 14% strand | Q5SHX3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.60 | 0.82 | 30 | empty |
| 2 | 220 | 0.55 | 0.78 | 33 | empty |
| 3 | 54 | 0.36 | 0.79 | 14 | CL |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5XT8 · Magnesium bound apo structure of thymidylate kinase (form I) 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 5XT8 · PDBe 5XT8 · UniProt Q5SHX3
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