Research workbench
Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and magnesium ions.
Analyse Crystal structure of mouse thiamine triphosphatase in complex with thiamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A65
- Type
- protein
- Length
- 405 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine triphosphatase
- EC
- 3.6.1.28
- UniProt
- Q8JZL3
- Ligands
- TPP, MG, PO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine triphosphatase (EC 3.6.1.28) | protein | 208 | 33% helix, 35% strand | Q8JZL3 |
| B | Thiamine triphosphatase (EC 3.6.1.28) | protein | 197 | 34% helix, 35% strand | Q8JZL3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.72 | 0.79 | 47 | MG, TPP, PO4 |
| 2 | 584 | 0.71 | 0.79 | 49 | MG, TPP, PO4 |
| 3 | 413 | 0.63 | 0.78 | 51 | empty |
| 4 | 119 | 0.45 | 0.78 | 26 | empty |
| 5 | 84 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 413 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A65 · Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8JZL3 · AlphaFold monomer V2.0 prediction for thiamine-triphosphatase (Q8JZL3) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q8JZL3
- Elsewhere: RCSB PDB 5A65 · PDBe 5A65 · UniProt Q8JZL3
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