SMTL ID : 9c1a.1

Crystal structure of GDP-bound human M-RAS protein in crystal form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION

MG.1: 2 residues within 4Å: Chain A: S.42 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.42, H2O.1, H2O.1, H2O.2, H2O.2 MG.6: 1 residues within 4Å: Chain A: K.51 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.51, H2O.3, H2O.3, H2O.6, H2O.7

1 x GDP: GUANOSINE-5'-DIPHOSPHATE

GDP.2: 20 residues within 4Å: Chain A: D.36, G.37, G.38, V.39, G.40, K.41, S.42, A.43, F.53, P.55, D.56, Y.57, N.141, K.142, D.144, L.145, S.171, A.172, K.173 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.38, A:V.39, A:G.40, A:K.41, A:S.42, A:A.43, A:D.56, A:D.56, A:Y.57, A:N.141, A:K.142, A:A.172, A:K.173 Water bridges: A:K.41, A:S.42, A:S.42, A:V.54, A:D.56, A:T.83, A:K.142, A:K.142, A:K.142 Salt bridges: A:K.41, A:D.144 pi-Stacking: A:F.53, A:F.53

3 x GOL: GLYCEROL

GOL.3: 4 residues within 4Å: Chain A: K.157, A.160, T.161, I.165 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.160, A:I.165 Water bridges: A:K.157, A:K.157, A:I.165 GOL.4: 1 residues within 4Å: Chain A: E.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.154, A:E.154 GOL.5: 2 residues within 4Å: Chain A: D.174, P.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.174 Water bridges: A:D.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bester, S.M. et al., Crystal structure of the GDP-bound human M-RAS protein in two crystal forms. Acta Crystallogr.,Sect.F (2024)

Release Date

2024-09-11

Peptides

Ras-related protein M-Ras: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ras-related protein M-Ras