Research workbench
Structure of streptococcus gordonii inorganic pyrophosphatase
Analyse Structure of streptococcus gordonii inorganic pyrophosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WPP
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable manganese-dependent inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P95765
- Ligands
- ZN, SO4, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 310 | 42% helix, 20% strand | P95765 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.76 | 0.83 | 59 | SO4 |
| 2 | 746 | 0.76 | 0.81 | 62 | SO4, CL |
| 3 | 157 | 0.58 | 0.82 | 24 | empty |
| 4 | 160 | 0.57 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1WPP · Structure of Streptococcus gordonii inorganic pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
- P95765 · AlphaFold monomer V2.0 prediction for probable manganese-dependent inorganic… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P95765
- Elsewhere: RCSB PDB 1WPP · PDBe 1WPP · UniProt P95765
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