SMTL ID : 3sea.3 (2 other biounits)

Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.4 MG.4: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.5, H2O.9 MG.7: 3 residues within 4Å: Chain C: S.18, D.58 Ligands: GDP.8 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.18, H2O.10, H2O.10, H2O.10, H2O.11 MG.9: 3 residues within 4Å: Chain D: S.18, D.58 Ligands: GDP.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.18, H2O.15, H2O.15, H2O.15, H2O.16

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

GNP.2: 23 residues within 4Å: Chain A: Y.12, R.13, S.14, V.15, G.16, K.17, S.18, S.19, F.29, V.30, D.31, A.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.147, A.148, K.149 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:S.19, A:S.19, A:V.30, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.148 Water bridges: A:S.18, A:S.18, A:S.18, A:D.58 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GNP.5: 23 residues within 4Å: Chain B: Y.12, R.13, S.14, V.15, G.16, K.17, S.18, S.19, F.29, V.30, D.31, A.33, P.35, T.36, G.61, N.117, K.118, D.120, L.121, S.147, A.148, K.149 Ligands: MG.4 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:S.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:S.19, B:S.19, B:V.30, B:T.36, B:G.61, B:N.117, B:K.118, B:K.118, B:A.148 Water bridges: B:S.18, B:S.18, B:T.36, B:D.58 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

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

ACT.3: 5 residues within 4Å: Chain A: S.18, A.33, D.34, T.36, N.39 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.33 Hydrogen bonds: A:S.18, A:S.18, A:D.34, A:N.39 Water bridges: A:T.36, A:I.37 ACT.6: 5 residues within 4Å: Chain B: S.18, A.33, D.34, T.36, N.39 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.33 Hydrogen bonds: B:S.18, B:S.18, B:D.34, B:N.39 Water bridges: B:T.36, B:I.37

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.8: 19 residues within 4Å: Chain C: Y.12, R.13, S.14, V.15, G.16, K.17, S.18, S.19, F.29, V.30, D.31, N.117, K.118, D.120, L.121, S.147, A.148, K.149 Ligands: MG.7 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:S.14, C:V.15, C:G.16, C:K.17, C:S.18, C:S.19, C:S.19, C:V.30, C:N.117, C:K.118, C:K.118, C:S.147, C:A.148 Water bridges: C:K.17, C:K.17, C:S.18, C:S.18, C:A.33, C:K.149, C:K.149 Salt bridges: C:K.17, C:D.120 pi-Stacking: C:F.29, C:F.29 pi-Cation interactions: C:K.118 GDP.10: 19 residues within 4Å: Chain D: Y.12, R.13, S.14, V.15, G.16, K.17, S.18, S.19, F.29, V.30, D.31, N.117, K.118, D.120, L.121, S.147, A.148, K.149 Ligands: MG.9 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:S.14, D:V.15, D:G.16, D:K.17, D:S.18, D:S.19, D:S.19, D:V.30, D:N.117, D:K.118, D:K.118, D:S.147, D:A.148 Water bridges: D:K.17, D:K.17, D:S.18, D:S.18, D:D.31, D:A.33, D:K.149, D:K.149 Salt bridges: D:K.17, D:D.120 pi-Stacking: D:F.29, D:F.29 pi-Cation interactions: D:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazhab-Jafari, M.T. et al., An Autoinhibited Noncanonical Mechanism of GTP Hydrolysis by Rheb Maintains mTORC1 Homeostasis. Structure (2012)

Release Date

2012-06-20

Peptides

GTP-binding protein Rheb: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

GTP-binding protein Rheb

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