MolNFT v1 · #73377 · protein
Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1 complexed with substrate G3P
3O07 · Pyridoxine biosynthesis protein SNZ1: “Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1 complexed with substrate G3P”. X-ray diffraction, 1 ligand (G3H), 9 pockets (best druggability 0.75). MolNFT v1 #73377 on…
- PDB
- 3O07
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine biosynthesis protein SNZ1
- UniProt
- Q03148
- Ligands
- G3H
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyridoxine biosynthesis protein SNZ1 | protein | 259 | 46% helix, 14% strand | Q03148 |
| B | Pyridoxine biosynthesis protein SNZ1 | protein | 257 | 43% helix, 14% strand | Q03148 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.75 | 0.83 | 61 | empty |
| 2 | 392 | 0.71 | 0.83 | 42 | empty |
| 3 | 265 | 0.70 | 0.85 | 40 | empty |
| 4 | 186 | 0.67 | 0.86 | 29 | empty |
| 5 | 82 | 0.41 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 907 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3O07 · Crystal structure of yeast pyridoxal 5-phosphate synthase Snz1 complexed with substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q03148 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit SNZ1… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q03148
- Elsewhere: RCSB PDB 3O07 · PDBe 3O07 · UniProt Q03148
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