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Crystal structure of D235A mutant of human pyridoxal kinase

Analyse Crystal structure of D235A mutant of human pyridoxal kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FHX
Type: protein
Length: 617 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: O00764
Ligands: ATP, PXL, PLP, MG, NA, SO4
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal kinase (EC 2.7.1.35)	protein	307	39% helix, 23% strand	O00764
B	Pyridoxal kinase (EC 2.7.1.35)	protein	310	40% helix, 23% strand	O00764

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 2 copies · chains A, B
PLP · Pyridoxal-5'-phosphate · ligand · chains B
MG · Magnesium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 11 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	876	0.78	0.81	68	MG, NA, ATP, PXL, SO4
2	859	0.78	0.81	64	MG, NA, ATP, PXL, PLP, SO4
3	82	0.76	0.99	16	empty
4	114	0.62	0.88	17	SO4
5	83	0.45	0.81	23	empty

Interfaces

1 interface between chains.

A–B · 2183 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

3FHX · Crystal structure of D235A mutant of human pyridoxal kinase · the same entry in another collection · chain A against A, TM-score 1.00
O00764 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (O00764) · 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 O00764
Elsewhere: RCSB PDB 3FHX · PDBe 3FHX · UniProt O00764

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