Research workbench
X-ray structure of a putative phosphoprotein phosphatase from arabidopsis thaliana gene AT1G05000
Analyse X-ray structure of a putative phosphoprotein phosphatase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XRI
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT1G05000
- UniProt
- Q9ZVN4
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AT1G05000 | protein | 151 | 48% helix, 15% strand | Q9ZVN4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, 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 | 53 | 0.51 | 0.88 | 17 | SO4 |
| 2 | 69 | 0.39 | 0.79 | 16 | empty |
| 3 | 65 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 877 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1XRI · X-ray structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZVN4 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase DSP1 (Q9ZVN4) · 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 Q9ZVN4
- Elsewhere: RCSB PDB 1XRI · PDBe 1XRI · UniProt Q9ZVN4
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