MolNFT v1 · #5049 · protein
Fluoride-inhibited substrate complex of saccharomyces cerevisiae inorganic pyrophosphatase
1E6A: “Fluoride-inhibited substrate complex of saccharomyces cerevisiae inorganic pyrophosphatase”. X-ray diffraction, 5 ligands (POP, MN, NA), 4 pockets (best druggability 0.65). MolNFT v1 #5049 on GenesisL1: 3D structure, binding sites…
- PDB
- 1E6A
- Type
- protein
- Length
- 566 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
- POP, MN, NA, F, PO4
- Pockets
- 4 · best druggability 0.65
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 | 284 | 20% helix, 31% strand | P00817 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 282 | 20% helix, 31% strand | P00817 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · chains A
- F · Fluoride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.65 | 0.75 | 47 | empty |
| 2 | 161 | 0.52 | 0.79 | 31 | MN, POP, PO4, F |
| 3 | 189 | 0.51 | 0.78 | 33 | MN, POP, F, NA |
| 4 | 51 | 0.47 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1E6A · Fluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase · 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 1E6A · PDBe 1E6A · UniProt P00817
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