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

H-Ras Set 1 CaCl2 'Mixed

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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.2 CA.4: 5 residues within 4Å: Chain A: R.102, V.103 Chain F: R.102, V.103 Ligands: CA.29 No protein-ligand interaction detected (PLIP) CA.6: 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.6, H2O.7 CA.9: 5 residues within 4Å: Chain B: R.102, V.103 Chain E: R.102, V.103 Ligands: CA.24 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Chain C: F.28, D.30 Chain F: E.31, D.33 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: F:E.31, C:F.28, C:D.30, H2O.10, H2O.11 CA.14: 5 residues within 4Å: Chain C: R.102, V.103 Chain D: R.102, V.103 Ligands: CA.19 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain B: E.31, D.33 Chain D: F.28, D.30 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:E.31, D:F.28, D:D.30, H2O.14, H2O.15 CA.19: 5 residues within 4Å: Chain C: R.102, V.103 Chain D: R.102, V.103 Ligands: CA.14 No protein-ligand interaction detected (PLIP) CA.21: 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.18, H2O.19 CA.24: 5 residues within 4Å: Chain B: R.102, V.103 Chain E: R.102, V.103 Ligands: CA.9 No protein-ligand interaction detected (PLIP) CA.26: 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.22, H2O.23 CA.29: 5 residues within 4Å: Chain A: R.102, V.103 Chain F: R.102, V.103 Ligands: CA.4 No protein-ligand interaction detected (PLIP)

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.17, T.35, D.57 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.17, A:T.35, H2O.1, H2O.1 MG.3: 1 residues within 4Å: Chain A: Q.129 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: S.17, T.35, D.57 Ligands: GNP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:T.35, H2O.5, H2O.5 MG.8: 1 residues within 4Å: Chain B: Q.129 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: S.17, T.35, D.57 Ligands: GNP.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.17, C:T.35, H2O.9, H2O.9 MG.13: 1 residues within 4Å: Chain C: Q.129 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain D: S.17, T.35, D.57 Ligands: GNP.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.17, D:T.35, H2O.13, H2O.13 MG.18: 1 residues within 4Å: Chain D: Q.129 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain E: S.17, T.35, D.57 Ligands: GNP.25 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.17, E:T.35, H2O.18, H2O.18 MG.23: 1 residues within 4Å: Chain E: Q.129 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain F: S.17, T.35, D.57 Ligands: GNP.30 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.17, F:T.35, H2O.22, H2O.22 MG.28: 1 residues within 4Å: Chain F: Q.129 No protein-ligand interaction detected (PLIP)

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

GNP.5: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 25 PLIP interactions: 25 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:T.58, 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.10: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.7 25 PLIP interactions: 25 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:T.58, 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.15: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.12 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:T.58, 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 Salt bridges: C:D.119 pi-Stacking: C:F.28, C:F.28 GNP.20: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.17 25 PLIP interactions: 25 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:T.58, 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.25: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.22 25 PLIP interactions: 25 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:T.58, 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.30: 27 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, T.58, A.59, G.60, Q.61, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.27 25 PLIP interactions: 25 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:T.58, 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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