SMTL ID : 8fo8.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

GDP.1: 16 residues within 4Å: Chain C: G.1344, S.1345, K.1347, T.1348, T.1349, M.1364, Q.1365, A.1367, T.1368, A.1396, G.1397, T.1452, H.1453, D.1455, N.1489, T.1491 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.1344, C:S.1345, C:K.1347, C:T.1348, C:T.1348, C:Q.1365, C:T.1368, C:G.1397, C:T.1452 Salt bridges: C:K.1347, C:K.1347, C:D.1455 GDP.3: 18 residues within 4Å: Chain D: 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.1344, D:S.1345, D:K.1347, D:T.1348, D:T.1348, D:Q.1365, D:T.1368, D:T.1368, D:G.1397, D:T.1452 Salt bridges: D:K.1347, D:K.1347, D:D.1455

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

ATP.2: 11 residues within 4Å: Chain C: G.1888, G.1891, V.1893, A.1904, K.1906, M.1947, E.1948, A.1950, S.1954, H.1998, L.2001 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.1948, C:A.1950, C:S.1954, C:S.1954 Salt bridges: C:K.1906 ATP.4: 12 residues within 4Å: Chain D: G.1888, G.1891, V.1893, A.1904, K.1906, M.1947, E.1948, L.1949, A.1950, S.1954, H.1998, L.2001 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.1948, D:A.1950, D:S.1954, D:S.1954, D:S.1954 Salt bridges: D:K.1906, D:H.1998

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

Ras-related protein Rab-7L1

Leucine-rich repeat serine/threonine-protein kinase 2

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