MolNFT v1 · #170821 · protein

Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma- S

6YK0: “Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma- S”. X-ray diffraction, 1 ligand (AGS), 15 pockets (best druggability 0.76). MolNFT v1 #170821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YK0
Type: protein
Length: 1,236 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: Q8K183
Ligands: AGS
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Pyridoxal kinase (EC 2.7.1.35)	protein	309	40% helix, 23% strand	Q8K183

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains A, B, C
PG4 · Tetraethylene glycol · additive · 2 copies · chains A

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.76	0.79	92	AGS, EDO
2	758	0.76	0.80	70	PG4, AGS
3	706	0.75	0.81	66	AGS, EDO
4	722	0.74	0.80	63	AGS, EDO
5	118	0.64	0.88	22	EDO

Interfaces

4 interfaces between chains.

A–B · 1940 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1932 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 324 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 78 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YK0 · Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S · the same entry in another collection · chain A against A, TM-score 1.00
Q8K183 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (Q8K183) · 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 Q8K183
Elsewhere: RCSB PDB 6YK0 · PDBe 6YK0 · UniProt Q8K183

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