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Crystal Structure of Pyridoxal Reductase (PDXI)

Analyse Crystal Structure of Pyridoxal Reductase (PDXI) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8TE8
Type: protein
Length: 565 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Escherichia coli
Molecule: Pyridoxine 4-dehydrogenase
EC: 1.1.1.65
UniProt: P25906
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxine 4-dehydrogenase (EC 1.1.1.65)	protein	282	41% helix, 18% strand	P25906
B	Pyridoxine 4-dehydrogenase (EC 1.1.1.65)	protein	283	43% helix, 20% strand	P25906

Pockets

6 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	217	0.59	0.80	38	empty
2	314	0.58	0.77	26	empty
3	220	0.56	0.79	37	empty
4	190	0.49	0.76	24	empty
5	66	0.47	0.84	17	empty

Interfaces

1 interface between chains.

A–B · 377 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

P25906 · AlphaFold monomer V2.0 prediction for pyridoxine 4-dehydrogenase (P25906) · 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 P25906
Elsewhere: RCSB PDB 8TE8 · PDBe 8TE8 · UniProt P25906

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