MolNFT v1 · #140512 · protein
Crystal structure of delta 4 mutant of ehpsat (phosphoserine aminotransferase of entamoeba histolytica)
5YD2: “Crystal structure of delta 4 mutant of ehpsat (phosphoserine aminotransferase of entamoeba histolytica)”. X-ray diffraction, 2 ligands (PLP, CL), 8 pockets (best druggability 0.77). MolNFT v1 #140512 on GenesisL1: 3D structure…
- PDB
- 5YD2
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine aminotransferase
- UniProt
- M7XC02
- Ligands
- PLP, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine aminotransferase | protein | 349 | 40% helix, 18% strand | M7XC02 |
| B | Phosphoserine aminotransferase | protein | 346 | 43% helix, 18% strand | M7XC02 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.77 | 0.82 | 90 | PLP |
| 2 | 502 | 0.75 | 0.83 | 67 | PLP |
| 3 | 50 | 0.68 | 0.97 | 19 | empty |
| 4 | 52 | 0.64 | 0.95 | 20 | empty |
| 5 | 117 | 0.56 | 0.83 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1899 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5YD2 · Crystal Structure of Delta 4 mutant of EhPSAT (Phosphoserine aminotransferase of… · 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 M7XC02
- Elsewhere: RCSB PDB 5YD2 · PDBe 5YD2 · UniProt M7XC02
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