- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CA: CALCIUM ION(Non-covalent)
- 18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.2: 3 residues within 4Å:- Chain A: S.17, T.35
- Ligands: GNP.4
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.3: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.6: 5 residues within 4Å:- Chain A: R.102, D.105
- Chain F: R.102, D.105
- Ligands: MG.36
5 PLIP interactions:2 interactions with chain A, 2 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: A:R.102, A:D.105, F:R.102, F:D.105, H2O.4
MG.8: 3 residues within 4Å:- Chain B: S.17, T.35
- Ligands: GNP.10
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.12: 5 residues within 4Å:- Chain B: R.102, D.105
- Chain E: R.102, D.105
- Ligands: MG.30
5 PLIP interactions:2 interactions with chain B, 2 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: B:R.102, B:D.105, E:R.102, E:D.105, H2O.10
MG.14: 3 residues within 4Å:- Chain C: S.17, T.35
- Ligands: GNP.16
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.18: 5 residues within 4Å:- Chain C: R.102, D.105
- Chain D: R.102, D.105
- Ligands: MG.24
5 PLIP interactions:2 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: C:R.102, C:D.105, D:R.102, D:D.105, H2O.17
MG.20: 3 residues within 4Å:- Chain D: S.17, T.35
- Ligands: GNP.22
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.24: 5 residues within 4Å:- Chain C: R.102, D.105
- Chain D: R.102, D.105
- Ligands: MG.18
5 PLIP interactions:2 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: C:R.102, C:D.105, D:R.102, D:D.105, H2O.24
MG.26: 3 residues within 4Å:- Chain E: S.17, T.35
- Ligands: GNP.28
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.30: 5 residues within 4Å:- Chain B: R.102, D.105
- Chain E: R.102, D.105
- Ligands: MG.12
5 PLIP interactions:2 interactions with chain B, 2 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: B:R.102, B:D.105, E:R.102, E:D.105, H2O.30
MG.32: 3 residues within 4Å:- Chain F: S.17, T.35
- Ligands: GNP.34
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)MG.36: 5 residues within 4Å:- Chain A: R.102, D.105
- Chain F: R.102, D.105
- Ligands: MG.6
5 PLIP interactions:2 interactions with chain A, 2 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: A:R.102, A:D.105, F:R.102, F:D.105, H2O.37
- 6 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)
GNP.4: 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.10: 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.16: 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.22: 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.28: 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.34: 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
- 6 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)
DTT.5: 5 residues within 4Å:- Chain A: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain A- Water bridges: A:D.92, A:Y.96
DTT.11: 5 residues within 4Å:- Chain B: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain B- Water bridges: B:D.92, B:Y.96
DTT.17: 5 residues within 4Å:- Chain C: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain C- Water bridges: C:D.92, C:Y.96
DTT.23: 5 residues within 4Å:- Chain D: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain D- Water bridges: D:D.92, D:Y.96
DTT.29: 5 residues within 4Å:- Chain E: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain E- Water bridges: E:D.92, E:Y.96
DTT.35: 5 residues within 4Å:- Chain F: R.68, D.92, Q.95, Y.96, Q.99
2 PLIP interactions:2 interactions with chain F- Water bridges: F:D.92, F:Y.96
- 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: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x CA: CALCIUM ION(Non-covalent)
- 18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 6 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)
- 6 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)
- 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: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
A