SMTL ID : 8cnj.1

HRas(1-166) in complex with GDP and BeF3-

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 22 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: BEF.2, MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.11, 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:D.33, A:T.35, A:T.35 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28 pi-Cation interactions: A:K.117 GDP.4: 23 residues within 4Å: Chain B: 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: BEF.5, MPD.6, MG.7 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:S.17, B:A.18, B:V.29, B:T.35, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Water bridges: B:T.35, B:T.35, B:K.147 Salt bridges: B:K.16, B:D.119 pi-Stacking: B:F.28, B:F.28 pi-Cation interactions: B:K.117

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

BEF.2: 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.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 13 residues within 4Å: Chain B: A.11, G.12, G.13, K.16, S.17, Y.32, P.34, T.35, A.59, G.60, Q.61 Ligands: GDP.4, MG.7 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.17, T.35 Ligands: GDP.1, BEF.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.2 MG.7: 4 residues within 4Å: Chain B: S.17, T.35 Ligands: GDP.4, BEF.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.7, H2O.7

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 8 residues within 4Å: Chain A: I.24 Chain B: S.17, I.21, V.29, E.31, Y.32, D.33 Ligands: GDP.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.33, A:I.24 Hydrogen bonds: B:D.33, B:D.33 Water bridges: B:D.33, B:T.35

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GTPase HRas

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