Research workbench
Yeast inorganic pyrophosphatase variant E48D with magnesium and phosphate
Analyse Yeast inorganic pyrophosphatase variant E48D with magnesium and phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IK0
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P00817
- Ligands
- MG, PO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 271 | 21% helix, 28% strand | P00817 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 286 | 20% helix, 31% strand | P00817 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.63 | 0.75 | 51 | empty |
| 2 | 330 | 0.59 | 0.77 | 41 | MG, PO4 |
| 3 | 56 | 0.48 | 0.85 | 19 | empty |
| 4 | 55 | 0.42 | 0.82 | 18 | empty |
| 5 | 113 | 0.42 | 0.78 | 19 | MG, PO4 |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2IK0 · Yeast inorganic pyrophosphatase variant E48D with magnesium and phosphate · 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 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 P00817
- Elsewhere: RCSB PDB 2IK0 · PDBe 2IK0 · UniProt P00817
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