MolNFT v1 · #182365 · protein
Crystal structure of arabidopsis thaliana plant and fungi atypical dual specificity phosphatase 1(ATPFA-DSP1 ) in complex with phosphate in conformation B (PI(B))
7MOL · Tyrosine-protein phosphatase DSP1: “Crystal structure of arabidopsis thaliana plant and fungi atypical dual specificity phosphatase 1(ATPFA-DSP1…”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.42). MolNFT v1…
- PDB
- 7MOL
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase DSP1
- EC
- 3.1.3.48
- UniProt
- Q9ZVN4
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase DSP1 (EC 3.1.3.48) | protein | 157 | 45% helix, 14% strand | Q9ZVN4 |
| B | Tyrosine-protein phosphatase DSP1 (EC 3.1.3.48) | protein | 153 | 45% helix, 14% strand | Q9ZVN4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.42 | 0.82 | 17 | PO4, EPE |
| 2 | 85 | 0.41 | 0.79 | 21 | PO4, EPE |
| 3 | 72 | 0.40 | 0.79 | 16 | empty |
| 4 | 51 | 0.35 | 0.79 | 13 | empty |
| 5 | 50 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1119 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7MOL · Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity… · 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 7MOL · PDBe 7MOL · UniProt Q9ZVN4
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