SMTL ID : 7pnc.1

Dark state structure of Sensory Rhodopsin II solved by serial millisecond crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 20 residues within 4Å: Chain A: Y.73, W.76, T.79, T.80, I.83, V.108, M.109, A.111, G.112, F.127, G.130, A.131, F.134, W.171, Y.174, P.175, W.178, D.201, T.204, K.205 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.80, A:V.108, A:F.127, A:F.127, A:F.134, A:W.171, A:W.171, A:Y.174, A:Y.174, A:Y.174, A:Y.174, A:P.175, A:P.175, A:W.178, A:K.205

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: V.68, F.69, R.72, Y.73, P.183 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: V.198, Y.199 Ligands: BOG.4, MPG.11 Ligand excluded by PLIP

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

BOG.3: 16 residues within 4Å: Chain A: I.46, V.49, A.50, V.53, V.58, G.59, W.60, V.61, A.70, P.71, I.74, D.75, L.78 Ligands: MPG.6, BOG.7, BOG.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.74 Hydrogen bonds: A:G.59 Water bridges: A:G.57, A:W.60 BOG.4: 9 residues within 4Å: Chain A: M.1, V.2, L.7, L.10, T.189, T.191, V.192, A.195 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.2 Water bridges: A:T.191 BOG.5: 11 residues within 4Å: Chain A: T.19, L.20, A.23, G.26, R.27, R.34, Y.37, V.38, V.41 Ligands: MPG.10, BOG.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.34, A:V.38 BOG.7: 6 residues within 4Å: Chain A: V.49, V.53, V.58 Ligands: BOG.3, BOG.8, MPG.10 No protein-ligand interaction detected (PLIP) BOG.8: 5 residues within 4Å: Chain A: L.56, V.58 Ligands: BOG.3, BOG.7, BOG.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.58 BOG.13: 4 residues within 4Å: Chain A: R.34, V.38 Ligands: BOG.5, MPG.10 No protein-ligand interaction detected (PLIP) BOG.15: 4 residues within 4Å: Chain A: W.9, I.13, L.56 Ligands: BOG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.56 BOG.16: 8 residues within 4Å: Chain A: L.110, F.113, A.114, M.117, V.118, P.119 Ligands: MPG.6, MPG.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.118, A:P.119

6 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.6: 16 residues within 4Å: Chain A: V.61, A.70, I.74, I.77, L.78, P.81, L.82, I.102, T.106, L.110, F.113, M.117 Ligands: BOG.3, MPG.9, MPG.10, BOG.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.77, A:P.81, A:P.81, A:L.82 MPG.9: 14 residues within 4Å: Chain A: S.95, G.99, I.102, T.103, T.106, V.107, L.110, A.111, A.114, L.126, M.129 Ligands: MPG.6, MPG.10, BOG.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.110 MPG.10: 18 residues within 4Å: Chain A: T.19, V.38, T.39, V.41, G.42, G.45, I.46, A.48, V.49, L.82, Y.85, S.95, F.98 Ligands: BOG.5, MPG.6, BOG.7, MPG.9, BOG.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.38, A:Y.85, A:F.98 MPG.11: 10 residues within 4Å: Chain A: R.162, Y.199, L.202, V.203, V.206, G.207, F.210, I.211, D.214 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.210, A:D.214 MPG.12: 6 residues within 4Å: Chain A: I.13, V.17, L.20, A.21, W.24, R.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.24 MPG.14: 6 residues within 4Å: Chain A: I.121, Y.124, A.125, F.127, G.128, L.179 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.121, A:F.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bosman, R. et al., Structural basis of the prolonged photocycle of Sensory Rhodopsin II revealed by serial millisecond crystallography. To Be Published

Release Date

2022-09-14

Peptides

Sensory rhodopsin-2: 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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Sensory rhodopsin-2

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