SMTL ID : 3v4f.1

H-Ras PEG 400/CaCl2, ordered off

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-hexamer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: F.28, D.30 Chain E: E.31, D.33 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:F.28, A:D.30, E:E.31, H2O.1, H2O.6 CA.5: 5 residues within 4Å: Chain A: R.102, D.105 Chain F: R.102, D.105 Ligands: CA.35 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Metal complexes: A:R.102, A:D.105, F:R.102, F:D.105 CA.7: 4 residues within 4Å: Chain B: F.28, D.30 Chain D: E.31, D.33 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:F.28, B:D.30, D:E.31, H2O.7, H2O.12 CA.11: 5 residues within 4Å: Chain B: R.102, D.105 Chain E: R.102, D.105 Ligands: CA.29 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Metal complexes: B:R.102, B:D.105, E:R.102, E:D.105 CA.13: 4 residues within 4Å: Chain C: F.28, D.30 Chain F: E.31, D.33 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: C:F.28, C:D.30, F:E.31, H2O.14, H2O.19 CA.17: 5 residues within 4Å: Chain C: R.102, D.105 Chain D: R.102, D.105 Ligands: CA.23 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:R.102, C:D.105, D:R.102, D:D.105 CA.19: 4 residues within 4Å: Chain B: E.31, D.33 Chain D: F.28, D.30 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:F.28, D:D.30, B:E.31, H2O.21, H2O.26 CA.23: 5 residues within 4Å: Chain C: R.102, D.105 Chain D: R.102, D.105 Ligands: CA.17 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:R.102, C:D.105, D:R.102, D:D.105 CA.25: 4 residues within 4Å: Chain A: E.31, D.33 Chain E: F.28, D.30 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: E:F.28, E:D.30, A:E.31, H2O.27, H2O.32 CA.29: 5 residues within 4Å: Chain B: R.102, D.105 Chain E: R.102, D.105 Ligands: CA.11 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Metal complexes: E:R.102, E:D.105, B:R.102, B:D.105 CA.31: 4 residues within 4Å: Chain C: E.31, D.33 Chain F: F.28, D.30 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: F:F.28, F:D.30, C:E.31, H2O.34, H2O.39 CA.35: 5 residues within 4Å: Chain A: R.102, D.105 Chain F: R.102, D.105 Ligands: CA.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Metal complexes: A:R.102, A:D.105, F:R.102, F:D.105

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

MG.2: 3 residues within 4Å: Chain A: S.17, T.35 Ligands: GNP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.6 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: S.17, T.35 Ligands: GNP.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.7, H2O.12 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: S.17, T.35 Ligands: GNP.18 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.17, C:T.35, H2O.14, H2O.19 MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain D: S.17, T.35 Ligands: GNP.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.21, H2O.26 MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain E: S.17, T.35 Ligands: GNP.30 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.17, E:T.35, H2O.27, H2O.32 MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain F: S.17, T.35 Ligands: GNP.36 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.17, F:T.35, H2O.34, H2O.39 MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.4: 5 residues within 4Å: Chain A: R.68, D.92, Q.95, Y.96, Q.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.95 Water bridges: A:Y.96 DTU.10: 5 residues within 4Å: Chain B: R.68, D.92, Q.95, Y.96, Q.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.95 Water bridges: B:Y.96 DTU.16: 5 residues within 4Å: Chain C: R.68, D.92, Q.95, Y.96, Q.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.95 Water bridges: C:Y.96 DTU.22: 5 residues within 4Å: Chain D: R.68, D.92, Q.95, Y.96, Q.99 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.95 DTU.28: 5 residues within 4Å: Chain E: R.68, D.92, Q.95, Y.96, Q.99 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.95 DTU.34: 5 residues within 4Å: Chain F: R.68, D.92, Q.95, Y.96, Q.99 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.95

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

GNP.6: 26 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 24 PLIP interactions: 24 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:Q.61, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:T.35, A:T.35 Salt bridges: A:D.119 pi-Stacking: A:F.28, A:F.28 GNP.12: 26 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.8 24 PLIP interactions: 24 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:Q.61, B:N.116, B:K.117, B:K.117, B:A.146, B:K.147 Water bridges: B:S.17, B:S.17, B:T.35, B:T.35 Salt bridges: B:D.119 pi-Stacking: B:F.28, B:F.28 GNP.18: 26 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.14 25 PLIP interactions: 25 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:Q.61, C:N.116, C:K.117, C:K.117, C:A.146, C:K.147 Water bridges: C:S.17, C:S.17, C:T.35, C:T.35, C:T.35 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28 GNP.24: 26 residues within 4Å: Chain D: 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.20 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:G.13, D:V.14, D:G.15, D:K.16, D:K.16, D:S.17, D:A.18, D:V.29, D:Y.32, D:Y.32, D:T.35, D:T.35, D:G.60, D:Q.61, D:N.116, D:K.117, D:K.117, D:A.146, D:K.147 Water bridges: D:S.17, D:S.17 Salt bridges: D:D.119 pi-Stacking: D:F.28, D:F.28 GNP.30: 26 residues within 4Å: Chain E: 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.26 24 PLIP interactions: 24 interactions with chain E Hydrogen bonds: E:G.13, E:V.14, E:G.15, E:K.16, E:K.16, E:S.17, E:A.18, E:V.29, E:Y.32, E:Y.32, E:T.35, E:T.35, E:G.60, E:Q.61, E:N.116, E:K.117, E:K.117, E:A.146, E:K.147 Water bridges: E:S.17, E:S.17 Salt bridges: E:D.119 pi-Stacking: E:F.28, E:F.28 GNP.36: 26 residues within 4Å: Chain F: 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, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.32 24 PLIP interactions: 24 interactions with chain F Hydrogen bonds: F:G.13, F:V.14, F:G.15, F:K.16, F:K.16, F:S.17, F:A.18, F:V.29, F:Y.32, F:Y.32, F:T.35, F:T.35, F:G.60, F:Q.61, F:N.116, F:K.117, F:K.117, F:A.146, F:K.147 Water bridges: F:S.17, F:S.17 Salt bridges: F:D.119 pi-Stacking: F:F.28, F:F.28

Links

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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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

GTPase HRas

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