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The structure of inorganic pyrophosphatase from schistosoma japonicum
Analyse The structure of inorganic pyrophosphatase from schistosoma japonicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QLZ
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SJCHGC07024 protein
- UniProt
- Q5DE13
- Ligands
- CO, PO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SJCHGC07024 protein | protein | 284 | 17% helix, 26% strand | Q5DE13 |
| B | SJCHGC07024 protein | protein | 283 | 16% helix, 28% strand | Q5DE13 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.59 | 0.80 | 35 | CO, PO4 |
| 2 | 227 | 0.55 | 0.78 | 36 | CO, PO4 |
| 3 | 71 | 0.50 | 0.84 | 17 | empty |
| 4 | 173 | 0.46 | 0.75 | 26 | empty |
| 5 | 117 | 0.39 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4QLZ · The structure of inorganic pyrophosphatase from Schistosoma japonicum · the same entry in another collection · chain A 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 Q5DE13
- Elsewhere: RCSB PDB 4QLZ · PDBe 4QLZ · UniProt Q5DE13
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