MolNFT v1 · #10987 · protein
Phospho-aspartyl intermediate analogue of phosphoserine phosphatase
1J97: “Phospho-aspartyl intermediate analogue of phosphoserine phosphatase”. X-ray diffraction, 2 ligands (MG, PO4), 3 pockets (best druggability 0.42). MolNFT v1 #10987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1J97
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine phosphatase
- EC
- 3.1.3.3
- UniProt
- Q58989
- Ligands
- MG, PO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine phosphatase (EC 3.1.3.3) | protein | 210 | 48% helix, 22% strand | Q58989 |
| B | Phosphoserine phosphatase (EC 3.1.3.3) | protein | 209 | 48% helix, 23% strand | Q58989 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.42 | 0.80 | 22 | empty |
| 2 | 92 | 0.40 | 0.78 | 27 | PO4 |
| 3 | 70 | 0.29 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1J97 · Phospho-Aspartyl Intermediate Analogue of Phosphoserine phosphatase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58989 · AlphaFold monomer V2.0 prediction for phosphoserine phosphatase (Q58989) · 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 Q58989
- Elsewhere: RCSB PDB 1J97 · PDBe 1J97 · UniProt Q58989
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