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Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives

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

PDB: 1YGJ
Type: protein
Length: 309 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: P82197
Ligands: RMC
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal kinase (EC 2.7.1.35)	protein	309	39% helix, 20% strand	P82197

Ligands and binding sites

RMC · (2R)-2-({6-[benzyl(methyl)amino]-9-isopropyl-9H-purin-2-yl}amino)butan-1-ol · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.75	0.81	64	RMC
2	127	0.42	0.76	17	empty

Compared structures

1YGJ · Crystal Structure of Pyridoxal Kinase in Complex with Roscovitine and Derivatives · the same entry in another collection · chain A against A, TM-score 1.00
P82197 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (P82197) · 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 P82197
Elsewhere: RCSB PDB 1YGJ · PDBe 1YGJ · UniProt P82197

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