MolNFT v1 · #40231 · protein
Yeast inorganic pyrophosphatase variant D120E with magnesium and phosphate
2IK6: “Yeast inorganic pyrophosphatase variant D120E with magnesium and phosphate”. X-ray diffraction, 2 ligands (MG, PO4), 6 pockets (best druggability 0.61). MolNFT v1 #40231 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IK6
- Type
- protein
- Length
- 550 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
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 268 | 21% helix, 30% strand | P00817 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 282 | 19% helix, 31% strand | P00817 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.61 | 0.74 | 51 | empty |
| 2 | 169 | 0.52 | 0.79 | 26 | MG, PO4 |
| 3 | 52 | 0.48 | 0.86 | 20 | empty |
| 4 | 59 | 0.45 | 0.83 | 18 | empty |
| 5 | 133 | 0.43 | 0.77 | 26 | MG, PO4 |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2IK6 · Yeast inorganic pyrophosphatase variant D120E 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 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 2IK6 · PDBe 2IK6 · UniProt P00817
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