MolNFT v1 · #26456 · protein
Crystal structure of the N-terminal core of bacillus subtilis inorganic pyrophosphatase
1WPN · Manganese-dependent inorganic pyrophosphatase: “Crystal structure of the N-terminal core of bacillus subtilis inorganic pyrophosphatase”. X-ray diffraction, 2 ligands (MN, SO4), 3 pockets (best druggability 0.43). MolNFT v1 #26456…
- PDB
- 1WPN
- Type
- protein
- Length
- 374 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
- MN, SO4
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 187 | 44% helix, 14% strand | P37487 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.43 | 0.75 | 26 | empty |
| 2 | 139 | 0.41 | 0.74 | 25 | empty |
| 3 | 57 | 0.34 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1WPN · Crystal structure of the N-terminal core 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 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 P37487
- Elsewhere: RCSB PDB 1WPN · PDBe 1WPN · UniProt P37487
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