Research workbench
Mouse thiamin pyrophosphokinase in a ternary complex with pyrithiamin pyrophosphate and AMP at 2.5 ångström
Analyse Mouse thiamin pyrophosphokinase in a ternary complex with pyrithiamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F17
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamin pyrophosphokinase 1
- EC
- 2.7.6.2
- UniProt
- Q9R0M5
- Ligands
- PYI, AMP, MG, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamin pyrophosphokinase 1 (EC 2.7.6.2) | protein | 255 | 24% helix, 32% strand | Q9R0M5 |
| B | Thiamin pyrophosphokinase 1 (EC 2.7.6.2) | protein | 243 | 25% helix, 34% strand | Q9R0M5 |
Ligands and binding sites
- PYI · 1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-{[hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-methylpyridinium · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.70 | 0.83 | 42 | SO4, PYI, AMP |
| 2 | 403 | 0.70 | 0.82 | 45 | MG, EPE, PYI |
| 3 | 100 | 0.48 | 0.81 | 18 | SO4 |
| 4 | 104 | 0.48 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1426 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2F17 · Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R0M5 · AlphaFold monomer V2.0 prediction for thiamin pyrophosphokinase 1 (Q9R0M5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9R0M5
- Elsewhere: RCSB PDB 2F17 · PDBe 2F17 · UniProt Q9R0M5
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