SMTL ID : 9f9e.1

Laser excitation effects on BR: Extrapolated 6 ps Light dataset recorded at 342 GW/cm2 at SwissFEL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

11 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: 5 residues within 4Å: Chain A: S.128, F.131, V.132, A.135 Ligands: LI1.15 No protein-ligand interaction detected (PLIP) LI1.2: 6 residues within 4Å: Chain A: Y.129, V.132, A.135, I.136, A.139 Ligands: LI1.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.132, A:I.136 LI1.3: 10 residues within 4Å: Chain A: A.10, T.13, A.14, G.17, L.18, F.50, L.54, L.57 Ligands: OLC.7, LI1.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.13, A:A.14, A:L.18, A:L.57 LI1.4: 2 residues within 4Å: Ligands: OLC.8, LI1.12 No protein-ligand interaction detected (PLIP) LI1.5: 2 residues within 4Å: Chain A: F.150 Ligands: LI1.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.150 LI1.6: 9 residues within 4Å: Chain A: F.149, N.172, V.175, V.176, S.179, A.180, V.183 Ligands: OLC.9, LI1.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.180, A:V.183 LI1.11: 7 residues within 4Å: Chain A: L.142, L.145, Y.146, F.149, F.150 Ligands: LI1.5, LI1.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.149, A:F.150 LI1.12: 2 residues within 4Å: Ligands: LI1.4, OLC.8 No protein-ligand interaction detected (PLIP) LI1.13: 7 residues within 4Å: Chain A: W.6, I.7, A.10, L.11, A.14, L.18 Ligands: LI1.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.7, A:A.10 LI1.14: 6 residues within 4Å: Chain A: P.87, L.88, L.91, I.104, V.108 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.91 LI1.15: 5 residues within 4Å: Chain A: S.128, Y.129, V.132 Ligands: LI1.1, LI1.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.132

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

OLC.7: 14 residues within 4Å: Chain A: G.17, T.20, L.21, L.24, G.27, K.36, Y.39, A.40, T.43, L.44, A.47, F.50, T.51 Ligands: LI1.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.21, A:L.24, A:T.43, A:F.50, A:F.50 OLC.8: 12 residues within 4Å: Chain A: L.44, I.48, T.51, M.52, Y.60, W.76, A.80, F.84, L.88 Ligands: LI1.4, LI1.12, LI1.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.48, A:W.76, A:F.84, A:L.88 Hydrogen bonds: A:Y.60 OLC.9: 12 residues within 4Å: Chain A: W.134, T.138, M.141, L.142, S.179, P.182, V.183, L.186, I.187, A.192, I.194 Ligands: LI1.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.134, A:L.186 OLC.10: 4 residues within 4Å: Chain A: I.199, L.202, L.203, V.206 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.199, A:L.203

1 x RET: RETINAL(Covalent)

RET.16: 19 residues within 4Å: Chain A: Y.79, W.82, T.85, T.86, L.89, M.114, I.115, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.79, A:W.82, A:T.86, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:W.185, A:K.212

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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