SMTL ID : 6wcw.1

Structure of human Rubicon RH domain in complex with GTP-bound Rab7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: S.19, G.20, V.21, G.22, K.23, T.24, S.25, F.35, S.36, N.37, Y.39, A.41, T.42, T.66, A.67, G.68, N.127, K.128, D.130, L.131, S.157, A.158, K.159 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.20, A:V.21, A:G.22, A:K.23, A:T.24, A:S.25, A:S.25, A:S.36, A:Y.39, A:T.42, A:T.42, A:G.68, A:N.127, A:K.128, A:K.128, A:S.157, A:A.158, A:K.159 Salt bridges: A:K.23, A:K.23, A:D.130 pi-Stacking: A:F.35, A:F.35 pi-Cation interactions: A:K.128

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.23, T.24, T.42, D.65, T.66 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.24, A:T.42

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.26, C.29, C.52, C.55 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.26, B:C.29, B:C.52, B:C.55 ZN.4: 5 residues within 4Å: Chain B: C.131, A.134, H.182, C.186, C.189 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.131, B:H.182, B:C.186, B:C.189 ZN.5: 4 residues within 4Å: Chain B: C.196, C.199, H.225, C.228 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.196, B:C.199, B:H.225, B:C.228 ZN.6: 4 residues within 4Å: Chain B: C.217, C.220, C.234, C.237 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.217, B:C.220, B:C.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhargava, H.K. et al., Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-01

Peptides

Ras-related protein Rab-7a: A
Run domain Beclin-1-interacting and cysteine-rich domain-containing protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Ras-related protein Rab-7a

Run domain Beclin-1-interacting and cysteine-rich domain-containing protein