Research workbench
Crystal Structure of a Novel-type Phosphoserine Phosphatase Mutant (H9A) from <i>Hydrogenobacter thermophilus</i> TK-6 in Complex with L-phosphoserine
Analyse Crystal Structure of a Novel-type Phosphoserine Phosphatase Mutant (H9A) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IJ6
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Hydrogenobacter thermophilus
- Molecule
- Phosphoserine phosphatase 1
- EC
- 3.1.3.3
- UniProt
- D3DFG8
- Ligands
- SEP, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine phosphatase 1 (EC 3.1.3.3) | protein | 207 | 47% helix, 20% strand | D3DFG8 |
| B | Phosphoserine phosphatase 1 (EC 3.1.3.3) | protein | 203 | 45% helix, 20% strand | D3DFG8 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.71 | 0.79 | 62 | SEP, CL |
| 2 | 293 | 0.56 | 0.76 | 34 | SEP, CL |
| 3 | 108 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1108 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4IJ6 · Crystal structure of a novel-type phosphoserine phosphatase mutant (H9A) from… · the same entry in another collection · chain A against A, TM-score 1.00
- D3DFG8 · AlphaFold monomer V2.0 prediction for phosphoserine phosphatase 1 (D3DFG8) · 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 D3DFG8
- Elsewhere: RCSB PDB 4IJ6 · PDBe 4IJ6 · UniProt D3DFG8
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