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Crystal structure of kinase

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

PDB: 5Y86
Type: protein
Length: 395 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity tyrosine-phosphorylation-regulated kinase 3
EC: 2.7.12.1
UniProt: O43781
Ligands: HRM, PO4
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity tyrosine-phosphorylation-regulated kinase 3 (EC 2.7.12.1)	protein	395	35% helix, 18% strand	O43781

Ligands and binding sites

HRM · 7-methoxy-1-methyl-9H-beta-carboline · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 8 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

3 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	436	0.68	0.80	50	HRM, EDO
2	71	0.36	0.77	13	empty
3	58	0.31	0.76	12	EDO

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

5Y86 · Crystal structure of kinase · the same entry in another collection · chain A against A, TM-score 1.00
O43781 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O43781
Elsewhere: RCSB PDB 5Y86 · PDBe 5Y86 · UniProt O43781

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