SMTL ID : 3lbn.2 (1 other biounit)

Ras soaked in Magnesium Acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 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:Y.32, 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 GNP.6: 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.8 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:Y.32, 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 GNP.11: 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.13 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:Y.32, 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

3 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.49, H2O.82 CA.7: 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.159, H2O.192 CA.12: 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.269, H2O.302

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.17, T.35, D.57 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.3, H2O.4 MG.4: 5 residues within 4Å: Chain A: Q.129 Chain B: Q.129 Chain C: Q.129 Ligands: MG.9, MG.14 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: Q.165 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: S.17, T.35, D.57 Ligands: GNP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.113, H2O.114 MG.9: 5 residues within 4Å: Chain A: Q.129 Chain B: Q.129 Chain C: Q.129 Ligands: MG.4, MG.14 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: Q.165 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: S.17, T.35, D.57 Ligands: GNP.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.17, C:T.35, H2O.223, H2O.224 MG.14: 5 residues within 4Å: Chain A: Q.129 Chain B: Q.129 Chain C: Q.129 Ligands: MG.4, MG.9 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain C: Q.165 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buhrman, G. et al., Allosteric modulation of Ras positions Q61 for a direct role in catalysis. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-03-02

Peptides

GTPase HRas: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

GTPase HRas

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