Research workbench
Crystal structure of type I inorganic pyrophosphatase from P falciparum
Analyse Crystal structure of type I inorganic pyrophosphatase from P falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WRU
- Type
- protein
- Length
- 1,543 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.193
- Source
- Plasmodium falciparum
- Molecule
- Probable inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- O77392
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · resolution 3.193 · 5 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable inorganic pyrophosphatase (EC 3.6.1.1) | protein | 310 | 19% helix, 31% strand | O77392 |
| B | Probable inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 19% helix, 31% strand | O77392 |
| C | Probable inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 18% helix, 30% strand | O77392 |
| D | Probable inorganic pyrophosphatase (EC 3.6.1.1) | protein | 306 | 17% helix, 27% strand | O77392 |
| E | Probable inorganic pyrophosphatase (EC 3.6.1.1) | protein | 311 | 19% helix, 32% strand | O77392 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.79 | 0.84 | 72 | empty |
| 2 | 513 | 0.75 | 0.83 | 52 | empty |
| 3 | 443 | 0.64 | 0.77 | 34 | empty |
| 4 | 251 | 0.56 | 0.78 | 35 | PO4 |
| 5 | 207 | 0.56 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3188 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3112 Ų buried · 60 hydrogen bonds · protein-protein
- A–E · 839 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 423 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5WRU · Crystal structure of type I inorganic pyrophosphatase from P falciparum · the same entry in another collection · chain E against E, TM-score 1.00
- O77392 · AlphaFold monomer V2.0 prediction for probable inorganic pyrophosphatase (O77392) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 O77392
- Elsewhere: RCSB PDB 5WRU · PDBe 5WRU · UniProt O77392
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