SMTL ID : 5lpn.1

Structure of human Rab10 in complex with the bMERB domain of Mical-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

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

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 24 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, T.38, F.40, I.41, S.42, T.43, G.69, N.124, K.125, D.127, M.128, S.154, A.155, K.156 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.21, A:V.22, A:G.23, A:K.24, A:K.24, A:T.25, A:C.26, A:N.37, A:T.43, A:T.43, A:G.69, A:N.124, A:K.125, A:K.125, A:A.155, A:K.156 Salt bridges: A:D.127 pi-Stacking: A:F.36, A:F.36 pi-Cation interactions: A:K.125 GNP.4: 24 residues within 4Å: Chain C: D.19, S.20, G.21, V.22, G.23, K.24, T.25, C.26, F.36, N.37, T.38, F.40, S.42, T.43, A.68, G.69, N.124, K.125, D.127, M.128, S.154, A.155, K.156 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:S.20, C:G.21, C:V.22, C:G.23, C:K.24, C:K.24, C:K.24, C:T.25, C:C.26, C:N.37, C:S.42, C:T.43, C:G.69, C:N.124, C:K.125, C:A.155, C:K.156, C:K.156 Water bridges: C:T.25 Salt bridges: C:D.127 pi-Stacking: C:F.36, C:F.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rai, A. et al., bMERB domains are bivalent Rab8 family effectors evolved by gene duplication. Elife (2016)

Release Date

2016-08-24

Peptides

Ras-related protein Rab-10: AC
Protein-methionine sulfoxide oxidase MICAL1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

Ras-related protein Rab-10

Protein-methionine sulfoxide oxidase MICAL1