SMTL ID : 8fo2.1

Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 monomer state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.20, T.21, T.39 Ligands: GNP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.39

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 19 residues within 4Å: Chain A: D.15, A.16, A.17, V.18, G.19, K.20, T.21, S.22, S.33, K.34, H.35, Y.36, K.37, S.38, T.39, K.126, V.156, K.157 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.17, A:V.18, A:G.19, A:K.20, A:K.20, A:T.21, A:T.21, A:S.22, A:S.22, A:S.22, A:H.35, A:K.37, A:K.37, A:T.39, A:T.39, A:K.126, A:K.157

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

GDP.3: 18 residues within 4Å: Chain B: G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, M.1364, Q.1365, A.1367, T.1368, F.1395, A.1396, G.1397, T.1452, H.1453, D.1455, N.1489, T.1491 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.1344, B:S.1345, B:K.1347, B:T.1348, B:Q.1365, B:T.1368, B:T.1368, B:F.1395, B:G.1397 Salt bridges: B:K.1347, B:K.1347, B:D.1455

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 12 residues within 4Å: Chain B: G.1888, G.1891, S.1892, V.1893, A.1904, K.1906, M.1947, E.1948, A.1950, S.1954, H.1998, L.2001 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.1892, B:E.1948, B:A.1950, B:S.1954, B:S.1954, B:S.1954 Salt bridges: B:K.1906

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science (2023)

Release Date

2024-01-03

Peptides

Ras-related protein Rab-7L1: A
Leucine-rich repeat serine/threonine-protein kinase 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

Ras-related protein Rab-7L1

Leucine-rich repeat serine/threonine-protein kinase 2

Related Entries With Identical Sequence