SMTL ID : 5b2z.1

H-Ras WT in complex with GppNHp (state 2*) before structural transition by humidity control

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

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

GNP.1: 26 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, P.39, T.40, A.64, G.65, Q.66, N.121, K.122, D.124, L.125, S.150, A.151, K.152 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.18, A:V.19, A:G.20, A:K.21, A:K.21, A:S.22, A:A.23, A:V.34, A:Y.37, A:T.40, A:G.65, A:Q.66, A:N.121, A:K.122, A:K.122, A:A.151, A:K.152 Water bridges: A:S.22, A:S.22, A:T.40, A:T.40 Salt bridges: A:D.124 pi-Stacking: A:F.33, A:F.33

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: F.33, D.35 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.33, A:D.35, H2O.6 CA.4: 2 residues within 4Å: Chain A: R.107, D.110 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.107, A:D.110, A:D.110, H2O.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.22, T.40 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.22, A:T.40, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, S. et al., Molecular Mechanism for Conformational Dynamics of Ras-GTP Elucidated from In-Situ Structural Transition in Crystal. Sci Rep (2016)

Release Date

2016-06-01

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas

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