SMTL ID : 6sge.1 (1 other biounit)

Crystal structure of Human RHOB-GTP in complex with nanobody B6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

GTP.1: 27 residues within 4Å: Chain A: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, Y.34, V.35, P.36, T.37, T.60, A.61, G.62, L.63, K.118, D.120, L.121, S.160, A.161, K.162 Chain B: L.111, N.113, Y.114 Ligands: MG.2 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.15, A:C.16, A:G.17, A:K.18, A:T.19, A:T.19, A:C.20, A:Y.34, A:T.37, A:T.37, A:G.62, A:K.118, A:K.118, A:S.160, A:A.161, A:K.162, B:N.113 Water bridges: A:T.19, A:L.21, A:E.32, A:V.33, A:Y.34, A:L.63, A:L.63, B:Y.114 Salt bridges: A:K.18, A:K.18, A:D.120 pi-Stacking: A:F.30

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.18, T.19, T.37 Ligands: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.19, A:T.37, H2O.1, H2O.3 MG.3: 7 residues within 4Å: Chain A: F.39, E.40, N.41, W.58, D.59, T.60, S.73 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.59, A:S.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bery, N. et al., A Targeted Protein Degradation Cell-Based Screening for Nanobodies Selective toward the Cellular RHOB GTP-Bound Conformation. Cell Chem Biol (2019)

Release Date

2019-09-25

Peptides

Rho-related GTP-binding protein RhoB: A
Nanobody B6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rho-related GTP-binding protein RhoB

Nanobody B6

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