SMTL ID : 2x72.1

CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.1: 6 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21, R.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain C: T.5, F.10, N.16, G.19, V.21, R.22 No protein-ligand interaction detected (PLIP)

2 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.2: 9 residues within 4Å: Chain A: Y.30, Y.97, L.100, H.101 Chain C: A.33, E.34, W.36, Q.37, M.40 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:W.36, C:W.36, C:W.36, A:Y.97, A:Y.97 Hydrogen bonds: A:Y.30, A:Y.30 Salt bridges: A:H.101 PEF.10: 9 residues within 4Å: Chain A: A.33, E.34, W.36, Q.37, M.40 Chain C: Y.30, Y.97, L.100, H.101 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.97, C:Y.97, A:W.36, A:W.36, A:W.36 Hydrogen bonds: C:Y.30 Salt bridges: C:H.101

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 7 residues within 4Å: Chain A: F.221, Y.224, G.225, K.232, K.249, T.252, V.255 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.221, A:Y.224, A:T.252, A:V.255 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.11: 7 residues within 4Å: Chain C: F.221, Y.224, G.225, K.232, K.249, T.252, V.255 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.221, C:Y.224, C:T.252, C:V.255 Hydrogen bonds: C:K.232 Salt bridges: C:K.232

4 x PLM: PALMITIC ACID(Covalent)

PLM.4: 14 residues within 4Å: Chain A: L.322, C.323, C.324 Chain C: L.47, L.48, L.51, R.253, I.257, T.298, Y.302, V.305, M.310 Ligands: PLM.5, LPP.7 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.47, C:L.48, C:L.51, C:I.257, C:T.298, C:V.305, C:V.305 Hydrogen bonds: C:R.253 PLM.5: 10 residues within 4Å: Chain A: L.322, C.323 Chain C: M.50, L.51, P.54, I.55, R.253, V.305, M.310 Ligands: PLM.4 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.51, C:P.54, C:I.55, C:V.305, A:L.322 Hydrogen bonds: C:R.253 PLM.12: 14 residues within 4Å: Chain A: L.47, L.48, L.51, R.253, I.257, T.298, Y.302, V.305, M.310 Chain C: L.322, C.323, C.324 Ligands: PLM.13, LPP.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.47, A:L.48, A:L.51, A:I.257, A:T.298, A:V.305, A:V.305 Hydrogen bonds: A:R.253 PLM.13: 10 residues within 4Å: Chain A: M.50, L.51, P.54, I.55, R.253, V.305, M.310 Chain C: L.322, C.323 Ligands: PLM.12 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.51, A:P.54, A:I.55, A:V.305, C:L.322 Hydrogen bonds: A:R.253

2 x RET: RETINAL(Non-covalent)

RET.6: 14 residues within 4Å: Chain A: A.118, T.119, C.188, G.189, I.190, Y.192, V.205, M.208, F.209, F.213, W.266, Y.269, A.270, A.273 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.190, A:Y.192, A:Y.192, A:V.205, A:M.208, A:F.209, A:F.213, A:W.266, A:Y.269, A:A.270, A:A.273 Water bridges: A:K.297 RET.14: 14 residues within 4Å: Chain C: A.118, T.119, C.188, G.189, I.190, Y.192, V.205, M.208, F.209, F.213, W.266, Y.269, A.270, A.273 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.190, C:Y.192, C:Y.192, C:V.205, C:M.208, C:F.209, C:F.213, C:W.266, C:Y.269, C:A.270, C:A.273 Water bridges: C:K.297

2 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)

LPP.7: 7 residues within 4Å: Chain C: R.253, I.257, V.259, I.260, A.261, Y.302 Ligands: PLM.4 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.259, C:I.260, C:I.260, C:A.261, C:Y.302 LPP.15: 7 residues within 4Å: Chain A: R.253, I.257, V.259, I.260, A.261, Y.302 Ligands: PLM.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.259, A:I.260, A:I.260, A:A.261, A:Y.302

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

ACT.8: 5 residues within 4Å: Chain A: V.205, I.206, F.209, F.274, F.277 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.206 ACT.16: 5 residues within 4Å: Chain C: V.205, I.206, F.209, F.274, F.277 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Standfuss, J. et al., The Structural Basis of Agonist Induced Activation in Constitutively Active Rhodopsin. Nature (2011)

Release Date

2011-03-16

Peptides

RHODOPSIN: AC
GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Membrane

We predict this structure to be a membrane protein.
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RHODOPSIN

GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1

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