Research workbench
Crystal structure of phosphoserine phosphatase mutant (H9A) from entamoeba histolytica in complex with phosphoserine
Analyse Crystal structure of phosphoserine phosphatase mutant (H9A) from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZR2
- Type
- protein
- Length
- 789 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase family protein, putative
- UniProt
- N9V397
- Ligands
- SEP, SO4
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Phosphoglycerate mutase family protein, putative | protein | 197 | 45% helix, 19% strand | N9V397 |
| C | Phosphoglycerate mutase family protein, putative | protein | 198 | 43% helix, 20% strand | N9V397 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.65 | 0.79 | 41 | SEP, SO4 |
| 2 | 350 | 0.65 | 0.79 | 32 | SEP, PEG |
| 3 | 224 | 0.61 | 0.81 | 31 | SEP |
| 4 | 228 | 0.60 | 0.80 | 28 | SEP, SO4 |
| 5 | 247 | 0.55 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 969 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZR2 · Crystal Structure of Phosphoserine Phosphatase Mutant (H9A) from Entamoeba histolytica in… · 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 5ZR2 · PDBe 5ZR2 · UniProt N9V397
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