MolNFT v1 · #85479 · protein
Crystal structure of plasmodial plp synthase complex
4ADS · Pyridoxine biosynthetic enzyme PDX1 homologue, putative: “Crystal structure of plasmodial plp synthase complex”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.78). MolNFT v1 #85479 on GenesisL1: 3D structure…
- PDB
- 4ADS
- Type
- protein
- Length
- 2,994 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine biosynthetic enzyme PDX1 homologue, putative; PDX2 protein
- UniProt
- Q4Z0E8, Q5ND68
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Pyridoxine biosynthetic enzyme PDX1 homologue, putative | protein | 282 | 43% helix, 14% strand | Q4Z0E8 |
| G, H, I, J, K, L | PDX2 protein | protein | 217 | 29% helix, 29% strand | Q5ND68 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.78 | 0.83 | 67 | PO4 |
| 2 | 650 | 0.78 | 0.84 | 67 | PO4 |
| 3 | 671 | 0.78 | 0.83 | 70 | PO4 |
| 4 | 658 | 0.78 | 0.83 | 71 | PO4 |
| 5 | 675 | 0.77 | 0.83 | 74 | PO4 |
Interfaces
12 interfaces between chains.
- E–H · 1502 Ų buried · 21 hydrogen bonds · protein-protein
- B–I · 1493 Ų buried · 16 hydrogen bonds · protein-protein
- F–K · 1483 Ų buried · 14 hydrogen bonds · protein-protein
- C–J · 1438 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 1426 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4ADS · Crystal structure of plasmodial PLP synthase complex · 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
- Every structure of UniProt Q5ND68
- Elsewhere: RCSB PDB 4ADS · PDBe 4ADS · UniProt Q4Z0E8 · UniProt Q5ND68
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.