MolNFT v1 · #27380 · protein
Thiamine phosphate pyrophosphorylase from pyrococcus furiosus pfu- 1255191-001
1XI3: “Thiamine phosphate pyrophosphorylase from pyrococcus furiosus pfu- 1255191-001”. X-ray diffraction, 3 ligands (NI, UNX, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #27380 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1XI3
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine phosphate pyrophosphorylase
- EC
- 2.5.1.3
- UniProt
- Q8U192
- Ligands
- NI, UNX, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thiamine phosphate pyrophosphorylase (EC 2.5.1.3) | protein | 202 | 45% helix, 18% strand | Q8U192 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains B
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.72 | 0.78 | 91 | SO4, UNX |
| 2 | 94 | 0.44 | 0.79 | 15 | empty |
| 3 | 89 | 0.43 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 864 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1XI3 · Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U192 · AlphaFold monomer V2.0 prediction for thiamine-phosphate synthase (Q8U192) · a predicted model of the same protein · chain A 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 Q8U192
- Elsewhere: RCSB PDB 1XI3 · PDBe 1XI3 · UniProt Q8U192
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