SMTL ID : 5b30.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

GNP.1: 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.2 26 PLIP interactions: 26 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: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, A:K.152, A:K.152 Salt bridges: A:D.124 pi-Stacking: A:F.33, A:F.33

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.22 Ligands: GNP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.22, H2O.1, H2O.2, H2O.6

2 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: R.107, D.110 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.107, A:D.110, A:D.110, H2O.1, H2O.5

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

NA.5: 2 residues within 4Å: Chain A: D.112, Y.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.112

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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