Research workbench
Crystal structure of inorganic pyrophosphatase (ppase) from pseudomonas aeruginosa
Analyse Crystal structure of inorganic pyrophosphatase (ppase) from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XEL
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q9HWZ6
- Ligands
- NA, MG, CL
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 172 | 17% helix, 34% strand | Q9HWZ6 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 170 | 18% helix, 36% strand | Q9HWZ6 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- 12P · Dodecaethylene glycol · additive · 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 | 260 | 0.57 | 0.78 | 40 | NA, MG |
| 2 | 240 | 0.56 | 0.78 | 41 | MG |
| 3 | 177 | 0.43 | 0.73 | 24 | 12P |
| 4 | 123 | 0.36 | 0.72 | 23 | empty |
| 5 | 86 | 0.35 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 292 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XEL · Crystal structure of Inorganic pyrophosphatase (PPase) from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HWZ6 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (Q9HWZ6) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q9HWZ6
- Elsewhere: RCSB PDB 4XEL · PDBe 4XEL · UniProt Q9HWZ6
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