SMTL ID : 7f6j.1

Crystal structure of the PDZD8 coiled-coil domain - Rab7 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.27, T.45, D.68 Ligands: GTP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.27, A:T.45, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain B: T.27, T.45 Ligands: GTP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.27, B:T.45, H2O.3, H2O.3

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

GTP.2: 25 residues within 4Å: Chain A: D.21, S.22, G.23, V.24, G.25, K.26, T.27, S.28, F.38, S.39, N.40, Q.41, Y.42, A.44, T.45, A.70, G.71, N.130, K.131, D.133, L.134, S.160, A.161, K.162 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.23, A:V.24, A:G.25, A:K.26, A:T.27, A:S.28, A:S.28, A:S.39, A:T.45, A:T.45, A:T.69, A:G.71, A:N.130, A:K.131, A:K.131, A:A.161, A:K.162 Water bridges: A:T.27, A:K.43, A:L.72, A:L.72 Salt bridges: A:K.26, A:K.26, A:D.133 pi-Stacking: A:F.38, A:F.38 GTP.4: 24 residues within 4Å: Chain B: D.21, S.22, G.23, V.24, G.25, K.26, T.27, S.28, F.38, S.39, N.40, Q.41, Y.42, K.43, A.44, T.45, N.130, K.131, D.133, L.134, S.160, A.161, K.162 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.23, B:V.24, B:G.25, B:K.26, B:T.27, B:S.28, B:S.28, B:Q.41, B:T.45, B:N.130, B:K.131, B:K.131, B:S.160, B:A.161, B:K.162 Water bridges: B:K.26, B:K.26, B:T.27, B:T.27 Salt bridges: B:K.26, B:K.26, B:D.133 pi-Stacking: B:F.38, B:F.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, H. et al., Structural basis of human PDZD8-Rab7 interaction for the ER-late endosome tethering. Sci Rep (2021)

Release Date

2022-02-23

Peptides

Ras-related protein Rab-7a: AB
PDZ domain-containing protein 8: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ras-related protein Rab-7a

PDZ domain-containing protein 8