SMTL ID : 5ax0.1

Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: W.97, T.100, T.101, L.104, M.129, G.133, F.148, G.151, C.152, L.155, W.192, Y.195, P.196, W.199, D.221, A.224, K.225 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.97, A:T.101, A:L.155, A:W.192, A:Y.195, A:Y.195, A:Y.195, A:Y.195, A:P.196, A:W.199, A:W.199, A:A.224, A:K.225

3 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.2: 11 residues within 4Å: Chain A: I.61, T.64, A.65, N.72, K.77, Y.91, A.92, I.95, D.96, F.99 Ligands: D10.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.61, A:I.61, A:T.64, A:A.65, A:A.92, A:I.95, A:I.95, A:F.99, A:F.99 Hydrogen bonds: A:N.72 Water bridges: A:A.92 OLB.3: 8 residues within 4Å: Chain A: L.18, V.190, L.191, V.212, I.215, I.219, L.223 Ligands: C14.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.190, A:L.191, A:I.219, A:I.219, A:L.223 Water bridges: A:D.211, A:D.211, A:V.212 OLB.4: 13 residues within 4Å: Chain A: V.98, F.99, P.102, L.103, L.106, V.109, L.110, T.112, N.113, M.114, I.119, I.127, K.173 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.98, A:F.99, A:P.102, A:L.103, A:L.106, A:I.119, A:I.119, A:I.127 Hydrogen bonds: A:M.114, A:K.173, A:K.173

2 x D12: DODECANE(Non-covalent)

D12.5: 2 residues within 4Å: Chain A: Q.42, F.43 No protein-ligand interaction detected (PLIP) D12.6: 5 residues within 4Å: Chain A: C.152, P.196, I.197, G.200 Ligands: R16.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.196, A:I.197

1 x C14: TETRADECANE(Non-covalent)

C14.7: 5 residues within 4Å: Chain A: I.219, L.223, L.227 Ligands: OLB.3, D10.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.219, A:L.223, A:L.227

1 x R16: HEXADECANE(Non-covalent)

R16.8: 5 residues within 4Å: Chain A: W.145, F.148, C.152, A.156 Ligands: D12.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.145, A:W.145, A:W.145, A:F.148, A:A.156

2 x D10: DECANE(Non-covalent)

D10.9: 6 residues within 4Å: Chain A: Y.53, I.56, A.57, T.60, T.64 Ligands: OLB.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.53, A:I.56, A:A.57, A:T.60 D10.10: 5 residues within 4Å: Chain A: I.219, L.222, P.226, L.227 Ligands: C14.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.219, A:L.222, A:P.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuse, M. et al., Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-08-26

Peptides

Rhodopsin I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin I

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