SMTL ID : 4cym.1 (5 other biounits)

Complex of human VARP-ANKRD1 with Rab32-GppCp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 24 residues within 4Å: Chain A: L.39, G.40, V.41, G.42, K.43, T.44, S.45, F.55, S.56, Q.57, H.58, Y.59, A.61, T.62, A.88, G.89, N.148, K.149, D.151, Q.152, S.179, A.180, K.181 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.40, A:V.41, A:G.42, A:K.43, A:K.43, A:T.44, A:S.45, A:S.45, A:S.56, A:Q.57, A:Y.59, A:T.62, A:G.89, A:N.148, A:K.149, A:K.149, A:Q.152, A:S.179, A:A.180, A:K.181 Water bridges: A:T.44, A:T.44, A:R.60 Salt bridges: A:D.151 pi-Stacking: A:F.55, A:F.55 GCP.3: 24 residues within 4Å: Chain C: L.39, G.40, V.41, G.42, K.43, T.44, S.45, F.55, S.56, Q.57, H.58, Y.59, A.61, T.62, A.88, G.89, N.148, K.149, D.151, Q.152, S.179, A.180, K.181 Ligands: MG.4 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.40, C:V.41, C:G.42, C:K.43, C:K.43, C:T.44, C:T.44, C:S.45, C:S.45, C:S.56, C:Q.57, C:T.62, C:G.89, C:N.148, C:K.149, C:K.149, C:Q.152, C:S.179, C:A.180, C:K.181 Water bridges: C:R.60, C:R.60 Salt bridges: C:D.151 pi-Stacking: C:F.55, C:F.55

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.44, T.62 Ligands: GCP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.44, A:T.62, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain C: T.44, T.62 Ligands: GCP.3 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.44, C:T.62, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hesketh, G.G. et al., Varp is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface. Dev.Cell (2014)

Release Date

2014-06-04

Peptides

RAS-RELATED PROTEIN RAB-32: AC
ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
D

D
D

RAS-RELATED PROTEIN RAB-32

ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27

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