SMTL ID : 7dph.1

H-Ras Q61H in complex with GppNHp (state 1) after structural transition by humidity control

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-trimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: S.22 Ligands: GNP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.22, H2O.1, H2O.2, H2O.4 MG.2: 2 residues within 4Å: Ligands: MG.6, MG.10 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: S.22 Ligands: GNP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.22, H2O.5, H2O.6, H2O.8 MG.6: 2 residues within 4Å: Ligands: MG.2, MG.10 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: S.22 Ligands: GNP.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.22, H2O.9, H2O.10, H2O.11 MG.10: 2 residues within 4Å: Ligands: MG.2, MG.6 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: D.112, Y.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.142 Water bridges: A:V.114 NA.7: 2 residues within 4Å: Chain B: D.112, Y.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.142 Water bridges: B:V.114 NA.11: 2 residues within 4Å: Chain C: D.112, Y.142 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.142 Water bridges: C:V.114

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

GNP.4: 23 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, A.64, G.65, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.1 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.18, A:V.19, A:G.20, A:K.21, A:K.21, A:S.22, A:A.23, A:E.36, A:Y.37, A:G.65, A:N.121, A:K.122, A:K.122, A:A.151, A:K.152 Water bridges: A:S.22, A:S.22, A:S.22, A:S.22, A:D.38, C:H.99 Salt bridges: A:D.124 pi-Stacking: A:F.33, A:F.33 GNP.8: 23 residues within 4Å: Chain B: 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, A.64, G.65, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.5 24 PLIP interactions: 1 interactions with chain A, 23 interactions with chain B Water bridges: A:H.99, B:S.22, B:S.22, B:S.22, B:S.22, B:D.38 Hydrogen bonds: B:G.18, B:V.19, B:G.20, B:K.21, B:K.21, B:S.22, B:A.23, B:E.36, B:Y.37, B:G.65, B:N.121, B:K.122, B:K.122, B:A.151, B:K.152 Salt bridges: B:D.124 pi-Stacking: B:F.33, B:F.33 GNP.12: 23 residues within 4Å: Chain C: 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, A.64, G.65, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.9 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.18, C:V.19, C:G.20, C:K.21, C:K.21, C:S.22, C:A.23, C:E.36, C:Y.37, C:G.65, C:N.121, C:K.122, C:K.122, C:A.151, C:K.152 Water bridges: C:S.22, C:S.22, C:S.22, C:S.22, C:D.38, B:H.99 Salt bridges: C:D.124 pi-Stacking: C:F.33, C:F.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, S. et al., Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-07-28

Peptides

GTPase HRas: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

GTPase HRas