SMTL ID : 5te3.2 (1 other biounit)

Crystal structure of Bos taurus opsin at 2.7 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 6 residues within 4Å: Chain B: T.4, F.9, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

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

BOG.2: 5 residues within 4Å: Chain A: F.220, K.231, T.251, V.254, I.255 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.220, A:T.251, A:V.254, A:I.255 Hydrogen bonds: A:K.231 Salt bridges: A:K.231 BOG.3: 6 residues within 4Å: Chain A: P.27, Y.96, L.99, H.100, Y.102 Chain B: W.35 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.35, B:W.35, B:W.35, B:W.35, A:Y.96, A:L.99 Salt bridges: A:H.100 BOG.8: 13 residues within 4Å: Chain A: A.117, T.118, G.121, C.187, G.188, I.189, Y.191, M.207, F.212, W.265, Y.268, A.269, A.272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.191, A:M.207, A:F.212, A:Y.268, A:A.269, A:A.272 Hydrogen bonds: A:C.187, A:I.189, A:Y.268 BOG.10: 5 residues within 4Å: Chain B: F.220, K.231, T.251, V.254, I.255 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.220, B:T.251, B:V.254, B:I.255 Hydrogen bonds: B:K.231 Salt bridges: B:K.231 BOG.11: 6 residues within 4Å: Chain A: W.35 Chain B: P.27, Y.96, L.99, H.100, Y.102 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.35, A:W.35, A:W.35, A:W.35, B:Y.96, B:L.99 Salt bridges: B:H.100 BOG.16: 13 residues within 4Å: Chain B: A.117, T.118, G.121, C.187, G.188, I.189, Y.191, M.207, F.212, W.265, Y.268, A.269, A.272 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.191, B:M.207, B:F.212, B:Y.268, B:A.269, B:A.272 Hydrogen bonds: B:C.187, B:I.189

4 x PLM: PALMITIC ACID(Covalent)

PLM.4: 7 residues within 4Å: Chain A: C.322, N.326 Chain B: T.297, Y.301, I.305, M.309 Ligands: PLM.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.297, B:Y.301, B:I.305 Hydrogen bonds: A:N.326 PLM.7: 9 residues within 4Å: Chain A: L.321, C.322, C.323 Chain B: I.259, I.263, T.297, Y.301, I.305 Ligands: PLM.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.259, B:I.263, B:T.297, B:Y.301, B:I.305 PLM.12: 7 residues within 4Å: Chain A: T.297, Y.301, I.305, M.309 Chain B: C.322, N.326 Ligands: PLM.15 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.297, A:Y.301, A:I.305 Hydrogen bonds: B:N.326 PLM.15: 9 residues within 4Å: Chain A: I.259, I.263, T.297, Y.301, I.305 Chain B: L.321, C.322, C.323 Ligands: PLM.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.259, A:I.263, A:T.297, A:Y.301, A:I.305

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: Q.36, I.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.36 SO4.6: 1 residues within 4Å: Chain A: Q.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.237, A:Q.237 SO4.13: 2 residues within 4Å: Chain B: Q.36, I.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.36 SO4.14: 1 residues within 4Å: Chain B: Q.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.237, B:Q.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gulati, S. et al., Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-15

Peptides

Rhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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