SMTL ID : 4dlu.2 (1 other biounit)

H-Ras Set 1 Ca(OAc)2, on

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

GNP.1: 25 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, P.34, T.35, A.59, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.3 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:K.16, A:S.17, A:A.18, A:V.29, A:T.35, A:G.60, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:D.33, A:T.35, A:T.35, A:Q.61, A:Q.61 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 pi-Cation interactions: A:K.117 GNP.7: 25 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, P.34, T.35, A.59, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.9 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:G.13, B:V.14, B:G.15, B:K.16, B:K.16, B:S.17, B:A.18, B:V.29, B:T.35, B:G.60, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Water bridges: B:S.17, B:S.17, B:D.33, B:T.35, B:T.35, B:Q.61, B:Q.61 Salt bridges: B:D.119 pi-Stacking: B:F.28, B:F.28 pi-Cation interactions: B:K.117 GNP.13: 25 residues within 4Å: Chain C: 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, P.34, T.35, A.59, G.60, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.15 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:G.13, C:V.14, C:G.15, C:K.16, C:K.16, C:S.17, C:A.18, C:V.29, C:T.35, C:G.60, C:N.116, C:K.117, C:K.117, C:A.146, C:K.147 Water bridges: C:S.17, C:S.17, C:D.33, C:T.35, C:T.35, C:Q.61, C:Q.61 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28 pi-Cation interactions: C:K.117

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: F.28, D.30 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.28, A:D.30, H2O.1, H2O.5 CA.4: 3 residues within 4Å: Chain A: D.107, Y.137 Ligands: ACT.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.107, A:Y.137, H2O.3, H2O.6, H2O.6 CA.8: 2 residues within 4Å: Chain B: F.28, D.30 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.28, B:D.30, H2O.8, H2O.13 CA.10: 3 residues within 4Å: Chain B: D.107, Y.137 Ligands: ACT.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.107, B:Y.137, H2O.10, H2O.13, H2O.14 CA.14: 2 residues within 4Å: Chain C: F.28, D.30 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:F.28, C:D.30, H2O.16, H2O.20 CA.16: 3 residues within 4Å: Chain C: D.107, Y.137 Ligands: ACT.18 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.107, C:Y.137, H2O.18, H2O.20, H2O.21

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: S.17, T.35 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.5 MG.5: 2 residues within 4Å: Ligands: MG.11, MG.17 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: S.17, T.35 Ligands: GNP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.8, H2O.12 MG.11: 2 residues within 4Å: Ligands: MG.5, MG.17 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: S.17, T.35 Ligands: GNP.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.17, C:T.35, H2O.15, H2O.20 MG.17: 2 residues within 4Å: Ligands: MG.5, MG.11 No protein-ligand interaction detected (PLIP)

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

ACT.6: 8 residues within 4Å: Chain A: R.97, K.101, D.107, D.108, V.109, M.111, Y.137 Ligands: CA.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.97, A:K.101 Hydrogen bonds: A:D.107, A:V.109 Water bridges: A:R.97 Salt bridges: A:R.97 ACT.12: 8 residues within 4Å: Chain B: R.97, K.101, D.107, D.108, V.109, M.111, Y.137 Ligands: CA.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.97, B:K.101 Hydrogen bonds: B:D.107, B:V.109 Water bridges: B:R.97 Salt bridges: B:R.97 ACT.18: 8 residues within 4Å: Chain C: R.97, K.101, D.107, D.108, V.109, M.111, Y.137 Ligands: CA.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.97, C:K.101 Hydrogen bonds: C:D.107, C:V.109 Water bridges: C:R.97 Salt bridges: C:R.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holzapfel, G. et al., Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition. Biochemistry (2012)

Release Date

2012-08-08

Peptides

GTPase HRas: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

GTPase HRas

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