Research workbench
Crystal structure of inorganic pyrophosphatase PPA1 from arabidopsis thaliana
Analyse Crystal structure of inorganic pyrophosphatase PPA1 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LS0
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble inorganic pyrophosphatase 1
- EC
- 3.6.1.1
- UniProt
- Q93V56
- Ligands
- MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble inorganic pyrophosphatase 1 (EC 3.6.1.1) | protein | 175 | 21% helix, 31% strand | Q93V56 |
| B | Soluble inorganic pyrophosphatase 1 (EC 3.6.1.1) | protein | 179 | 22% helix, 30% strand | Q93V56 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.73 | 0.77 | 68 | MG |
| 2 | 121 | 0.48 | 0.80 | 24 | MG |
| 3 | 56 | 0.43 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5LS0 · Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q93V56 · AlphaFold monomer V2.0 prediction for soluble inorganic pyrophosphatase 1 (Q93V56) · 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 Q93V56
- Elsewhere: RCSB PDB 5LS0 · PDBe 5LS0 · UniProt Q93V56
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