MolNFT v1 · #113131 · protein
Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and magnesium ions.
5A65: “Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and…”. X-ray diffraction, 3 ligands (TPP, MG, PO4), 5 pockets (best druggability 0.72). MolNFT v1 #113131 on GenesisL1: 3D…
- 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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