SMTL ID : 8cnn.1

BeF3 Phospho-HRas GSA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: R.68, D.92, Q.95, Y.96, Q.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.68 PEG.3: 5 residues within 4Å: Chain A: T.148, R.149, Q.150, G.151 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.148, A:G.151 Water bridges: A:G.151

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

ACT.2: 3 residues within 4Å: Chain A: R.149, E.153 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.153 Salt bridges: A:R.149 ACT.4: 2 residues within 4Å: Chain A: K.147 Ligands: GDP.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.147 ACT.5: 1 residues within 4Å: Chain A: R.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.73

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.6: 23 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: ACT.4, BEF.7, MG.8 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:V.29, A:Y.32, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:D.33, A:T.35, A:T.35 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.7: 12 residues within 4Å: Chain A: G.12, G.13, K.16, S.17, Y.32, P.34, T.35, A.59, G.60, Q.61 Ligands: GDP.6, MG.8 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: S.17, T.35 Ligands: GDP.6, BEF.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.2

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: S.106, D.108, H.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.106, A:S.106 Salt bridges: A:H.166 SO4.10: 2 residues within 4Å: Chain A: H.94, Q.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.95 Water bridges: A:H.94 Salt bridges: A:H.94 SO4.11: 3 residues within 4Å: Chain A: R.97, K.101, Y.137 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.97, A:K.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baumann, P. et al., Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3 - complexes. Commun Chem (2024)

Release Date

2023-09-27

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase HRas

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