Research workbench
Crystal structure of inorganic pyrophosphatase from staphylococcus aureus in complex with MN2+
Analyse Crystal structure of inorganic pyrophosphatase from staphylococcus aureus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RPA
- Type
- protein
- Length
- 616 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
- D9RMT1
- Ligands
- MN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 40% helix, 21% strand | D9RMT1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.85 | 0.91 | 64 | empty |
| 2 | 673 | 0.84 | 0.88 | 88 | empty |
| 3 | 498 | 0.64 | 0.77 | 68 | empty |
| 4 | 57 | 0.27 | 0.73 | 16 | empty |
| 5 | 58 | 0.26 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4RPA · Crystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with… · 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 D9RMT1
- Elsewhere: RCSB PDB 4RPA · PDBe 4RPA · UniProt D9RMT1
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