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
- 4LUG
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q93V56
- Ligands
- NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 175 | 21% helix, 31% strand | Q93V56 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 176 | 21% helix, 31% strand | Q93V56 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.71 | 0.77 | 55 | NA |
| 2 | 124 | 0.49 | 0.80 | 23 | empty |
| 3 | 112 | 0.49 | 0.80 | 20 | empty |
| 4 | 118 | 0.47 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4LUG · 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 B 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 4LUG · PDBe 4LUG · UniProt Q93V56
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