SMTL ID : 6gyh.1

Crystal structure of the light-driven proton pump Coccomyxa subellipsoidea Rhodopsin CsR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: W.87, T.91, L.94, M.119, G.123, Y.138, S.141, F.145, W.182, Y.185, P.186, W.189, D.211, A.214, K.215 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.87, A:W.87, A:T.91, A:Y.138, A:F.145, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:W.189, A:A.214, A:K.215 RET.7: 15 residues within 4Å: Chain B: W.87, T.91, L.94, M.119, G.123, Y.138, S.141, F.145, W.182, Y.185, P.186, W.189, D.211, A.214, K.215 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.87, B:W.87, B:T.91, B:Y.138, B:F.145, B:W.182, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:W.189, B:A.214, B:K.215 RET.13: 15 residues within 4Å: Chain C: W.87, T.91, L.94, M.119, G.123, Y.138, S.141, F.145, W.182, Y.185, P.186, W.189, D.211, A.214, K.215 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.87, C:W.87, C:T.91, C:Y.138, C:F.145, C:W.182, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:W.189, C:A.214, C:K.215

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 11 residues within 4Å: Chain A: A.67, Y.81, I.85, F.88, F.89, M.121, L.128 Ligands: OLB.4, CLR.8, CLR.14, OLB.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.81, A:I.85, A:F.89, A:L.128 CLR.8: 11 residues within 4Å: Chain B: A.67, Y.81, I.85, F.88, F.89, M.121, L.128 Ligands: CLR.2, OLB.4, OLB.10, CLR.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.81, B:I.85, B:F.89, B:L.128 CLR.14: 11 residues within 4Å: Chain C: A.67, Y.81, I.85, F.88, F.89, M.121, L.128 Ligands: CLR.2, CLR.8, OLB.10, OLB.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.81, C:I.85, C:F.89, C:L.128

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

OLB.3: 10 residues within 4Å: Chain A: A.118, F.125, L.128 Chain B: I.52, A.56, A.59, G.64, G.65, A.82, I.85 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.52, B:A.56, B:I.85, B:I.85, A:F.125, A:F.125, A:F.125, A:L.128 OLB.4: 9 residues within 4Å: Chain A: F.88, M.121, F.125, L.128 Chain B: Y.81, I.85, F.89 Ligands: CLR.2, CLR.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.88, A:F.125, A:L.128, B:I.85, B:F.89 OLB.5: 8 residues within 4Å: Chain A: W.135, Y.138, G.139, C.142, A.143, F.146, V.147, W.150 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.135, A:W.135, A:Y.138 OLB.6: 4 residues within 4Å: Chain A: A.205, S.206, G.209, L.210 No protein-ligand interaction detected (PLIP) OLB.9: 10 residues within 4Å: Chain B: A.118, F.125, L.128 Chain C: I.52, A.56, A.59, G.64, G.65, A.82, I.85 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.52, C:A.56, C:I.85, C:I.85, B:F.125, B:F.125, B:F.125, B:L.128 OLB.10: 9 residues within 4Å: Chain B: F.88, M.121, F.125, L.128 Chain C: Y.81, I.85, F.89 Ligands: CLR.8, CLR.14 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.85, C:F.89, B:F.88, B:F.125, B:L.128 OLB.11: 8 residues within 4Å: Chain B: W.135, Y.138, G.139, C.142, A.143, F.146, V.147, W.150 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.135, B:W.135, B:Y.138 OLB.12: 4 residues within 4Å: Chain B: A.205, S.206, G.209, L.210 No protein-ligand interaction detected (PLIP) OLB.15: 10 residues within 4Å: Chain A: I.52, A.56, A.59, G.64, G.65, A.82, I.85 Chain C: A.118, F.125, L.128 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.125, C:F.125, C:F.125, C:L.128, A:I.52, A:A.56, A:I.85, A:I.85 OLB.16: 9 residues within 4Å: Chain A: Y.81, I.85, F.89 Chain C: F.88, M.121, F.125, L.128 Ligands: CLR.2, CLR.14 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.88, C:F.125, C:L.128, A:I.85, A:F.89 OLB.17: 8 residues within 4Å: Chain C: W.135, Y.138, G.139, C.142, A.143, F.146, V.147, W.150 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.135, C:W.135, C:Y.138 OLB.18: 4 residues within 4Å: Chain C: A.205, S.206, G.209, L.210 No protein-ligand interaction detected (PLIP)

Links

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Citation

Fudim, R. et al., Design of a light-gated proton channel based on the crystal structure ofCoccomyxarhodopsin. Sci.Signal. (2019)

Release Date

2019-03-27

Peptides

Family A G protein-coupled receptor-like protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Family A G protein-coupled receptor-like protein