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Structure of the LRRK2 dimer

Analyse Structure of the LRRK2 dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7LHT
Type
protein
Length
3,590 residues
Chains
2
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Leucine-rich repeat SERINE/THREONINE-protein kinase 2
EC
2.7.11.1, 3.6.5.-
UniProt
Q5S007
Ligands
GDP, ATP
Pockets
20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 27% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BLeucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 3.6.5.-)protein179527% helix, 15% strandQ5S007

Ligands and binding sites

  • GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
  • ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18690.820.84110ATP
211040.810.82110ATP
310090.780.7970empty
410270.770.7969empty
58660.760.8066empty

Interfaces

1 interface between chains.

  • A–B · 1494 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

  • 7LHT · Structure of the LRRK2 dimer · the same entry in another collection · chain A against A, TM-score 1.00
  • Q5S007 · AlphaFold monomer V2.0 prediction for leucine-rich repeat SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.61

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