Research workbench
Crystal structure of phosphoserine phosphatase from entamoeba histolytica
Analyse Crystal structure of phosphoserine phosphatase from entamoeba histolytica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZKK
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase family protein, putative
- UniProt
- N9V397
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglycerate mutase family protein, putative | protein | 197 | 43% helix, 20% strand | N9V397 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.62 | 0.79 | 29 | PO4, 144 |
| 2 | 278 | 0.59 | 0.79 | 27 | PO4 |
| 3 | 150 | 0.47 | 0.77 | 19 | PEG |
| 4 | 122 | 0.46 | 0.78 | 17 | PEG |
Interfaces
1 interface between chains.
- A–B · 931 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5ZKK · Crystal structure of Phosphoserine phosphatase from Entamoeba histolytica · the same entry in another collection · chain A against A, TM-score 1.00
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 N9V397
- Elsewhere: RCSB PDB 5ZKK · PDBe 5ZKK · UniProt N9V397
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