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Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1

Analyse Crystal structure of yeast pyridoxal 5-phosphate synthase SNZ1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3O06
Type: protein
Length: 774 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxine biosynthesis protein SNZ1
UniProt: Q03148
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Pyridoxine biosynthesis protein SNZ1	protein	258	46% helix, 13% strand	Q03148

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.76	0.82	65	empty
2	495	0.74	0.82	57	empty
3	199	0.67	0.86	33	empty
4	81	0.42	0.79	16	empty
5	77	0.39	0.78	16	empty

Interfaces

2 interfaces between chains.

B–C · 911 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 906 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3O06 · Crystal Structure of yeast pyridoxal 5-phosphate synthase Snz1 · 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 0.98

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 3O06 · PDBe 3O06 · UniProt Q03148

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