Research workbench
The R78K and D117E active site variants of saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications
Analyse The R78K and D117E active site variants of saccharomyces cerevisiae soluble… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8PRK
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (inorganic pyrophosphatase)
- EC
- 3.6.1.1
- UniProt
- P00817
- Ligands
- MN, PO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (inorganic pyrophosphatase) (EC 3.6.1.1) | protein | 282 | 19% helix, 31% strand | P00817 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.66 | 0.76 | 46 | empty |
| 2 | 187 | 0.58 | 0.81 | 28 | MN, PO4 |
| 3 | 199 | 0.56 | 0.80 | 33 | MN, PO4 |
| 4 | 53 | 0.48 | 0.85 | 20 | empty |
| 5 | 58 | 0.45 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 8PRK · The R78K and D117E active site variants of saccharomyces cerevisiae soluble inorganic… · the same entry in another collection · chain A against A, TM-score 1.00
- P00817 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P00817) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P00817
- Elsewhere: RCSB PDB 8PRK · PDBe 8PRK · UniProt P00817
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