SMTL ID : 5wdq.1

H-Ras mutant L120A bound to GMP-PNP at 100K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

GNP.1: 29 residues within 4Å: Chain A: A.15, G.16, G.17, V.18, G.19, K.20, S.21, A.22, F.32, V.33, D.34, E.35, Y.36, D.37, P.38, T.39, A.63, G.64, Q.65, N.120, K.121, D.123, A.124, S.149, A.150, K.151 Ligands: CA.2, MG.3, ACT.6 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.17, A:V.18, A:G.19, A:K.20, A:K.20, A:S.21, A:S.21, A:A.22, A:V.33, A:Y.36, A:Y.36, A:T.39, A:T.39, A:G.64, A:Q.65, A:N.120, A:K.121, A:K.121, A:S.149, A:A.150, A:K.151 Water bridges: A:S.21, A:D.34 Salt bridges: A:D.123 pi-Stacking: A:F.32, A:F.32

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: K.20, S.21, T.39 Ligands: GNP.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.21, A:T.39, H2O.1, H2O.2 CA.4: 3 residues within 4Å: Chain A: F.32, V.33, D.34 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:F.32, A:D.34

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: K.20, S.21, T.39 Ligands: GNP.1, CA.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.21, A:T.39, H2O.1, H2O.2 MG.8: 1 residues within 4Å: Chain A: Q.169 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: R.106, V.107, D.109 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.106, A:D.109, A:D.109, H2O.6 MG.10: 1 residues within 4Å: Chain A: Q.133 No protein-ligand interaction detected (PLIP)

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

NA.5: 4 residues within 4Å: Chain A: K.92, E.95, D.96, Q.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.92, A:E.95 Water bridges: A:E.95, A:Q.99

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: N.89, D.123, A.124, A.125, K.151 Ligands: GNP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.89, A:A.125 Water bridges: A:A.126 ACT.7: 7 residues within 4Å: Chain A: L.27, N.30, K.46, V.48, R.153, E.157, Y.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.153, A:Y.161 Salt bridges: A:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bandaru, P. et al., Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife (2017)

Release Date

2017-07-19

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas