SMTL ID : 7kdc.2 (1 other biounit)

The complex between RhoD and the Plexin B2 RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: D.22, G.23, G.24, C.25, G.26, K.27, T.28, S.29, F.39, P.40, E.41, Y.43, P.45, T.46, T.69, G.71, L.72, K.127, D.129, L.130, S.169, A.170, R.171 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.24, A:C.25, A:G.26, A:K.27, A:K.27, A:T.28, A:T.28, A:S.29, A:S.29, A:P.40, A:Y.43, A:Y.43, A:T.46, A:G.71, A:K.127, A:K.127, A:A.170, A:R.171, A:R.171 Water bridges: A:T.28, A:D.68 Salt bridges: A:D.129 pi-Stacking: A:F.39, A:F.39

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.28, T.44, T.46, D.68 Ligands: GNP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.28, A:T.46, H2O.1 MG.3: 2 residues within 4Å: Chain A: D.73, D.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation. Elife (2021)

Release Date

2021-07-28

Peptides

Rho-related GTP-binding protein RhoD: A
Plexin-B2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Rho-related GTP-binding protein RhoD

Plexin-B2

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