SMTL ID : 6ojf.1

Dimeric structure of LRRK2 GTPase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.34 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.34, H2O.2, H2O.2, H2O.3, H2O.5 MG.3: 6 residues within 4Å: Chain A: M.24, M.95, T.96, A.99, Y.101, A.128 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:M.95, A:Y.101 MG.4: 3 residues within 4Å: Chain A: T.54 Chain B: T.34 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.34, H2O.1, H2O.1, H2O.2, H2O.6 MG.6: 4 residues within 4Å: Chain B: M.24, M.95, Y.101, R.127 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.95, B:Y.101, H2O.6

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 16 residues within 4Å: Chain A: N.28, T.29, G.30, S.31, G.32, K.33, T.34, T.35, T.138, H.139, D.141, V.174, N.175, A.176, T.177 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.28, A:G.30, A:S.31, A:G.32, A:K.33, A:T.34, A:T.34, A:T.35, A:T.35, A:H.139, A:N.175, A:A.176 Water bridges: A:K.33, A:T.35 Salt bridges: A:K.33, A:D.141 pi-Stacking: A:H.139, A:H.139 pi-Cation interactions: A:H.139 GDP.5: 15 residues within 4Å: Chain B: T.29, G.30, S.31, G.32, K.33, T.34, T.35, T.138, H.139, D.141, V.174, N.175, A.176, T.177 Ligands: MG.4 19 PLIP interactions: 2 interactions with chain A, 17 interactions with chain B Water bridges: A:T.54, A:T.54, B:K.33, B:T.34, B:T.34 Hydrogen bonds: B:G.30, B:S.31, B:G.32, B:K.33, B:T.34, B:T.35, B:T.35, B:H.139, B:N.175, B:A.176 Salt bridges: B:K.33, B:D.141 pi-Stacking: B:H.139, B:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, C.X. et al., Structural basis for conformational plasticity in the GTPase domain of the Parkinson's disease-associated protein LRRK2. To be published

Release Date

2020-10-14

Peptides

Leucine-rich repeat serine/threonine-protein kinase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Leucine-rich repeat serine/threonine-protein kinase 2