Research workbench
Yeast inorganic pyrophosphatase with magnesium and phosphate
Analyse Yeast inorganic pyrophosphatase 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
- 2IHP
- Type
- protein
- Length
- 558 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 · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 275 | 20% helix, 30% strand | P00817 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 283 | 20% helix, 32% strand | P00817 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
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 | 570 | 0.63 | 0.75 | 51 | empty |
| 2 | 284 | 0.59 | 0.79 | 34 | MG, MES |
| 3 | 121 | 0.49 | 0.80 | 22 | MG, PO4 |
| 4 | 59 | 0.45 | 0.83 | 17 | empty |
| 5 | 52 | 0.45 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1046 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 2IHP · PDBe 2IHP · UniProt P00817
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