MolNFT v1 · #142037 · protein
Crystal structure of phosphoserine phosphatase mutant (H9A) from entamoeba histolytica in complex with phosphoserine
5ZR2 · Phosphoglycerate mutase family protein, putative: “Crystal structure of phosphoserine phosphatase mutant (H9A) from entamoeba histolytica in complex with…”. X-ray diffraction, 2 ligands (SEP, SO4), 9 pockets (best druggability…
- 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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