SMTL ID : 2z73.4 (3 other biounits)

Crystal structure of squid rhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

BOG.1: 14 residues within 4Å: Chain A: T.67, A.69, N.70, I.73, R.133, K.146, E.256, L.259, I.262, S.263, Y.315, K.321, D.347, E.351 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.69, A:I.262, A:Y.315 Hydrogen bonds: A:T.67, A:K.321, A:D.347, A:E.351, A:E.351 BOG.8: 14 residues within 4Å: Chain B: T.67, A.69, N.70, I.73, R.133, K.146, E.256, L.259, I.262, S.263, Y.315, K.321, D.347, E.351 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.69, B:I.262, B:Y.315 Hydrogen bonds: B:T.67, B:K.321, B:D.347, B:E.351, B:E.351

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

SO4.2: 4 residues within 4Å: Chain A: S.148, R.150, R.151 Chain B: R.139 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.139, A:K.145, A:R.151 Hydrogen bonds: A:S.148 SO4.9: 4 residues within 4Å: Chain A: R.139 Chain B: S.148, R.150, R.151 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.148 Salt bridges: B:K.145, B:R.151, A:R.139

2 x RET: RETINAL(Covalent)

RET.3: 17 residues within 4Å: Chain A: N.87, Y.111, G.112, G.115, G.116, G.119, F.120, N.185, C.186, S.187, F.188, M.204, F.205, F.209, W.274, A.278, K.305 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.111, A:F.120, A:F.120, A:F.188, A:F.205, A:F.209, A:F.209, A:F.209, A:W.274, A:W.274, A:W.274, A:W.274, A:A.278, A:K.305 RET.10: 17 residues within 4Å: Chain B: N.87, Y.111, G.112, G.115, G.116, G.119, F.120, N.185, C.186, S.187, F.188, M.204, F.205, F.209, W.274, A.278, K.305 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.111, B:F.120, B:F.120, B:F.188, B:F.205, B:F.209, B:F.209, B:F.209, B:W.274, B:W.274, B:W.274, B:W.274, B:A.278, B:K.305

4 x PLM: PALMITIC ACID(Non-covalent)(Covalent)

PLM.4: 4 residues within 4Å: Chain A: I.56, K.61, F.78, F.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.56, A:F.78 Hydrogen bonds: A:K.61 PLM.5: 5 residues within 4Å: Chain A: M.313, S.316, V.317, V.333, C.337 No protein-ligand interaction detected (PLIP) PLM.11: 4 residues within 4Å: Chain B: I.56, K.61, F.78, F.81 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.56, B:F.78 Hydrogen bonds: B:K.61 PLM.12: 5 residues within 4Å: Chain B: M.313, S.316, V.317, V.333, C.337 No protein-ligand interaction detected (PLIP)

2 x TWT: DOCOSANE(Non-covalent)

TWT.6: 5 residues within 4Å: Chain A: I.46, G.51, F.89, P.312, M.313 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.89 TWT.13: 5 residues within 4Å: Chain B: I.46, G.51, F.89, P.312, M.313 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.89

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.7: 9 residues within 4Å: Chain A: R.193, S.195, R.198, S.199, L.202 Chain B: L.161, L.165, F.172, W.174 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:R.198, A:L.202, B:L.161, B:W.174, B:W.174 Salt bridges: A:R.198, A:R.198 PC1.14: 9 residues within 4Å: Chain A: L.161, L.165, F.172, W.174 Chain B: R.193, S.195, R.198, S.199, L.202 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.161, A:W.174, A:W.174, B:R.198, B:L.202 Salt bridges: B:R.198, B:R.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M. et al., Crystal structure of squid rhodopsin. Nature (2008)

Release Date

2008-05-13

Peptides

Rhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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