SMTL ID : 6xaf.1

1.9A crystal structure of the GTPase domain of Parkinson's disease-associated protein LRRK2 carrying R1398H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 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.1, H2O.1, H2O.2, H2O.3 MG.3: 2 residues within 4Å: Chain B: T.34 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.34, H2O.1, H2O.4, H2O.4, H2O.5

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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.30, A:S.31, A:G.32, A:K.33, A:T.34, A:T.35, A:T.35, A:H.139, A:N.175, A:A.176 Water bridges: A:K.33, A:K.33, A:T.35 Salt bridges: A:K.33, A:D.141 pi-Stacking: A:H.139, A:H.139 GDP.4: 15 residues within 4Å: Chain B: N.28, T.29, G.30, S.31, G.32, K.33, T.34, T.35, H.139, D.141, V.174, N.175, A.176, T.177 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.28, 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 Water bridges: B:K.33, B:K.33, B:K.33, B:T.35 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

2021-06-09

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