SMTL ID : 5vbe.1

Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 21 residues within 4Å: Chain A: A.16, G.17, G.18, V.19, G.20, K.21, S.22, A.23, F.33, V.34, D.35, E.36, Y.37, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.18, A:V.19, A:G.20, A:K.21, A:S.22, A:A.23, A:V.34, A:Y.37, A:N.121, A:K.122, A:K.122, A:A.151, A:K.152 Water bridges: A:K.21, A:Y.37 Salt bridges: A:K.21, A:D.124 pi-Stacking: A:F.33, A:F.33

1 x 92V: 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide(Covalent)

92V.2: 15 residues within 4Å: Chain A: V.12, V.14, T.63, G.65, Q.66, R.73, C.77, F.83, K.93, D.97, Q.100, Y.101, Q.104, I.105, V.108 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.101, A:Q.104 Hydrogen bonds: A:R.73, A:R.73 pi-Stacking: A:Y.101

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.22, Y.37, P.39, A.64 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.22, H2O.1, H2O.1, H2O.1, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gentile, D.R. et al., Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. Cell Chem Biol (2017)

Release Date

2017-10-25

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas

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