Research workbench
Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1 complxed with substrate plp
Analyse Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1 complxed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O05
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine biosynthesis protein SNZ1
- UniProt
- Q03148
- Ligands
- PLP
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pyridoxine biosynthesis protein SNZ1 | protein | 261 | 45% helix, 13% strand | Q03148 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.76 | 0.92 | 36 | empty |
| 2 | 174 | 0.75 | 0.92 | 37 | empty |
| 3 | 159 | 0.74 | 0.92 | 35 | empty |
| 4 | 179 | 0.64 | 0.85 | 31 | empty |
| 5 | 182 | 0.57 | 0.81 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 937 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3O05 · Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP · 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 A against A, TM-score 0.99
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 3O05 · PDBe 3O05 · UniProt Q03148
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