SMTL ID : 9f9c.1

Laser excitation effects on BR: Reprocessed Extrapolated 16 ns Light dataset recorded at 0.04 GW/cm2 from Nango et al.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

13 x LI1: 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL(Non-covalent)(Non-functional Binders)

LI1.1: 3 residues within 4Å: Chain A: Y.130, V.133, I.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.133, A:I.137 LI1.2: 7 residues within 4Å: Chain A: A.11, T.14, A.15, L.19, F.51, L.58 Ligands: OLC.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.11, A:A.15, A:L.19 LI1.3: 1 residues within 4Å: Ligands: OLC.7 No protein-ligand interaction detected (PLIP) LI1.4: 2 residues within 4Å: Chain A: F.151 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.151 LI1.5: 7 residues within 4Å: Chain A: F.150, V.176, V.177, S.180, A.181, V.184 Ligands: OLC.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.150, A:V.176 LI1.10: 5 residues within 4Å: Chain A: Y.128, S.129, F.132, V.133, A.136 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.128, A:A.136 LI1.11: 4 residues within 4Å: Chain A: A.140, L.143, Y.144, Y.147 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.147, A:Y.147 LI1.12: 6 residues within 4Å: Chain A: S.211, G.215, L.218, I.219, R.222 Ligands: LI1.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.218, A:I.219 LI1.13: 10 residues within 4Å: Chain A: L.16, L.19, G.20, Y.23, V.210, V.214, G.215, L.218, R.222 Ligands: LI1.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.23, A:Y.23, A:Y.23, A:L.218 LI1.14: 5 residues within 4Å: Chain A: I.8, A.11, L.12, A.15 Ligands: LI1.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.8, A:A.15 LI1.15: 8 residues within 4Å: Chain A: L.84, F.85, P.88, L.89, L.92, I.105, V.109 Ligands: OLC.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.85, A:P.88, A:V.109 LI1.16: 5 residues within 4Å: Chain A: L.12, L.16, V.207 Ligands: OLC.9, LI1.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.12, A:L.16 LI1.17: 1 residues within 4Å: Chain A: Y.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.23

4 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.6: 13 residues within 4Å: Chain A: G.18, T.21, L.22, L.25, G.28, K.37, Y.40, A.41, T.44, L.45, A.48, F.51 Ligands: LI1.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.22, A:T.44, A:F.51 Hydrogen bonds: A:K.37 OLC.7: 11 residues within 4Å: Chain A: L.45, I.49, T.52, M.53, Y.61, W.77, A.81, F.85, L.89 Ligands: LI1.3, LI1.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.77, A:F.85 Water bridges: A:W.77 OLC.8: 16 residues within 4Å: Chain A: W.135, T.139, M.142, L.143, L.146, Y.147, F.150, F.151, V.176, S.180, P.183, V.184, L.187, I.188 Ligands: LI1.4, LI1.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.143, A:V.184, A:L.187 OLC.9: 8 residues within 4Å: Chain A: I.195, V.196, P.197, I.200, L.203, L.204, V.207 Ligands: LI1.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.200, A:L.203

1 x RET: RETINAL(Covalent)

RET.18: 20 residues within 4Å: Chain A: Y.80, W.83, T.86, T.87, L.90, M.115, I.116, G.119, W.135, S.138, T.139, M.142, L.178, W.179, Y.182, P.183, W.186, D.209, A.212, K.213 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.80, A:T.87, A:W.179, A:Y.182, A:Y.182, A:Y.182, A:Y.182, A:Y.182, A:P.183, A:W.186, A:K.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertrand, Q. et al., Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate. Nat Commun (2024)

Release Date

2025-01-22

Peptides

Bacteriorhodopsin: 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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Bacteriorhodopsin

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