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Human DYRK1A/HARMINE complex

Analyse Human DYRK1A/HARMINE complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ANR
Type: protein
Length: 1,365 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
EC: 2.7.12.1
UniProt: Q13627
Ligands: HRM
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	343	35% helix, 18% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	343	36% helix, 18% strand	Q13627
C	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	338	36% helix, 18% strand	Q13627
D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	341	35% helix, 18% strand	Q13627

Ligands and binding sites

HRM · 7-methoxy-1-methyl-9H-beta-carboline · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 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	1162	0.85	0.86	130	empty
2	1081	0.84	0.84	101	empty
3	819	0.78	0.82	86	HRM
4	868	0.78	0.81	97	HRM
5	710	0.78	0.82	90	HRM

Interfaces

6 interfaces between chains.

A–B · 1260 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1228 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 821 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 788 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 61 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

3ANR · human DYRK1A/harmine complex · the same entry in another collection · chain D against D, TM-score 1.00
Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · 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 Q13627
Elsewhere: RCSB PDB 3ANR · PDBe 3ANR · UniProt Q13627

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