Research workbench
Structure of bacillus subtilis inorganic pyrophosphatase
Analyse Structure of bacillus subtilis inorganic pyrophosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WPM
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese-dependent inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P37487
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 307 | 41% helix, 21% strand | P37487 |
| B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 42% helix, 20% strand | P37487 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.80 | 0.93 | 47 | SO4 |
| 2 | 220 | 0.78 | 0.92 | 53 | SO4 |
| 3 | 221 | 0.48 | 0.74 | 35 | PG4 |
| 4 | 131 | 0.48 | 0.79 | 23 | empty |
| 5 | 216 | 0.48 | 0.74 | 41 | PG4 |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1WPM · Structure of Bacillus subtilis inorganic pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
- P37487 · AlphaFold monomer V2.0 prediction for manganese-dependent inorganic pyrophosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P37487
- Elsewhere: RCSB PDB 1WPM · PDBe 1WPM · UniProt P37487
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