Research workbench
Crystal structure of plasmodial plp synthase with bound R5P intermediate
Analyse Crystal structure of plasmodial plp synthase with bound R5P intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ADU
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine biosynthetic enzyme PDX1 homologue, putative
- UniProt
- Q4Z0E8
- Ligands
- R5P
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine biosynthetic enzyme PDX1 homologue, putative | protein | 278 | 46% helix, 14% strand | Q4Z0E8 |
| B | Pyridoxine biosynthetic enzyme PDX1 homologue, putative | protein | 274 | 43% helix, 14% strand | Q4Z0E8 |
Ligands and binding sites
- R5P · Ribose-5-phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.72 | 0.97 | 25 | R5P |
| 2 | 68 | 0.71 | 0.97 | 24 | R5P |
| 3 | 120 | 0.46 | 0.78 | 26 | empty |
| 4 | 72 | 0.36 | 0.77 | 20 | empty |
| 5 | 72 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ADU · Crystal structure of plasmodial PLP synthase with bound R5P intermediate · 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 Q4Z0E8
- Elsewhere: RCSB PDB 4ADU · PDBe 4ADU · UniProt Q4Z0E8
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