SMTL ID : 6rir.1

Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 26 residues within 4Å: Chain A: D.19, S.20, G.21, V.22, G.23, K.24, T.25, C.26, F.36, N.37, S.38, T.39, F.40, S.42, T.43, T.67, A.68, G.69, N.124, K.125, D.127, V.128, S.154, A.155, K.156 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.21, A:V.22, A:G.23, A:K.24, A:T.25, A:T.25, A:C.26, A:T.39, A:T.43, A:T.43, A:T.67, A:G.69, A:N.124, A:K.125, A:K.125, A:S.154, A:A.155, A:K.156 Water bridges: A:T.25, A:I.41, A:I.41, A:L.70 Salt bridges: A:K.24, A:K.24, A:D.127 pi-Stacking: A:F.36, A:F.36 GTP.4: 25 residues within 4Å: Chain B: D.19, S.20, G.21, V.22, G.23, K.24, T.25, C.26, F.36, N.37, S.38, F.40, S.42, T.43, T.67, A.68, G.69, N.124, K.125, D.127, V.128, S.154, A.155, K.156 Ligands: MG.5 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.21, B:V.22, B:G.23, B:K.24, B:T.25, B:T.25, B:C.26, B:N.37, B:T.43, B:T.43, B:T.67, B:G.69, B:N.124, B:K.125, B:K.125, B:A.155, B:K.156 Water bridges: B:T.25, B:L.70 Salt bridges: B:K.24, B:K.24, B:D.127 pi-Stacking: B:F.36, B:F.36

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.25, T.43 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.25, A:T.43, H2O.1, H2O.3 MG.5: 4 residues within 4Å: Chain B: T.25, T.43, D.66 Ligands: GTP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.25, B:T.43, H2O.7, H2O.9

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.13, W.65, Y.80, G.83, A.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.13, A:G.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waschbusch, D. et al., Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2. Structure (2020)

Release Date

2020-01-29

Peptides

Ras-related protein Rab-8A: AB
RILP-like protein 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Ras-related protein Rab-8A

RILP-like protein 2

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