SMTL ID : 9f9g.1

Laser excitation effects on BR: Reprocessed Dark from Nogly et al.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-trimer

Ligands

36 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: 2 residues within 4Å: Chain A: F.132, A.136 Ligand excluded by PLIP LI1.2: 9 residues within 4Å: Chain A: Y.130, V.133, I.137 Chain B: F.51, L.55, L.58, L.59 Ligands: LI1.21, OLC.25 Ligand excluded by PLIP LI1.3: 8 residues within 4Å: Chain A: A.11, T.14, A.15, L.19, F.51, L.58 Ligands: OLC.7, LI1.38 Ligand excluded by PLIP LI1.4: 9 residues within 4Å: Chain C: T.64, W.77, A.81, L.84, F.85, L.120, L.124 Ligands: OLC.8, OLC.44 Ligand excluded by PLIP LI1.5: 1 residues within 4Å: Chain A: F.151 Ligand excluded by PLIP LI1.6: 8 residues within 4Å: Chain A: F.150, N.173, V.176, V.177, S.180, A.181, V.184 Ligands: OLC.11 Ligand excluded by PLIP LI1.12: 7 residues within 4Å: Chain A: L.178, S.211, G.215, L.218, I.219, R.222 Ligands: LI1.13 Ligand excluded by PLIP LI1.13: 6 residues within 4Å: Chain A: Y.23, V.210, V.214, G.215, L.218 Ligands: LI1.12 Ligand excluded by PLIP LI1.14: 5 residues within 4Å: Chain A: I.8, A.11, L.12, A.15 Ligands: LI1.15 Ligand excluded by PLIP LI1.15: 5 residues within 4Å: Chain A: L.12, L.16, V.207, V.210 Ligands: LI1.14 Ligand excluded by PLIP LI1.16: 8 residues within 4Å: Chain A: L.143, Y.144, L.146, Y.147, F.150, F.151 Chain B: L.25, M.29 Ligand excluded by PLIP LI1.17: 3 residues within 4Å: Chain A: L.22, Y.23, V.26 Ligand excluded by PLIP LI1.19: 2 residues within 4Å: Chain B: F.132, A.136 Ligand excluded by PLIP LI1.20: 9 residues within 4Å: Chain B: Y.130, V.133, I.137 Chain C: F.51, L.55, L.58, L.59 Ligands: LI1.39, OLC.43 Ligand excluded by PLIP LI1.21: 8 residues within 4Å: Chain B: A.11, T.14, A.15, L.19, F.51, L.58 Ligands: LI1.2, OLC.25 Ligand excluded by PLIP LI1.22: 9 residues within 4Å: Chain A: T.64, W.77, A.81, L.84, F.85, L.120, L.124 Ligands: OLC.8, OLC.26 Ligand excluded by PLIP LI1.23: 1 residues within 4Å: Chain B: F.151 Ligand excluded by PLIP LI1.24: 8 residues within 4Å: Chain B: F.150, N.173, V.176, V.177, S.180, A.181, V.184 Ligands: OLC.29 Ligand excluded by PLIP LI1.30: 7 residues within 4Å: Chain B: L.178, S.211, G.215, L.218, I.219, R.222 Ligands: LI1.31 Ligand excluded by PLIP LI1.31: 6 residues within 4Å: Chain B: Y.23, V.210, V.214, G.215, L.218 Ligands: LI1.30 Ligand excluded by PLIP LI1.32: 5 residues within 4Å: Chain B: I.8, A.11, L.12, A.15 Ligands: LI1.33 Ligand excluded by PLIP LI1.33: 5 residues within 4Å: Chain B: L.12, L.16, V.207, V.210 Ligands: LI1.32 Ligand excluded by PLIP LI1.34: 8 residues within 4Å: Chain B: L.143, Y.144, L.146, Y.147, F.150, F.151 Chain C: L.25, M.29 Ligand excluded by PLIP LI1.35: 3 residues within 4Å: Chain B: L.22, Y.23, V.26 Ligand excluded by PLIP LI1.37: 2 residues within 4Å: Chain C: F.132, A.136 Ligand excluded by PLIP LI1.38: 9 residues within 4Å: Chain A: F.51, L.55, L.58, L.59 Chain C: Y.130, V.133, I.137 Ligands: LI1.3, OLC.7 Ligand excluded by PLIP LI1.39: 8 residues within 4Å: Chain C: A.11, T.14, A.15, L.19, F.51, L.58 Ligands: LI1.20, OLC.43 Ligand excluded by PLIP LI1.40: 9 residues within 4Å: Chain B: T.64, W.77, A.81, L.84, F.85, L.120, L.124 Ligands: OLC.26, OLC.44 Ligand excluded by PLIP LI1.41: 1 residues within 4Å: Chain C: F.151 Ligand excluded by PLIP LI1.42: 8 residues within 4Å: Chain C: F.150, N.173, V.176, V.177, S.180, A.181, V.184 Ligands: OLC.47 Ligand excluded by PLIP LI1.48: 7 residues within 4Å: Chain C: L.178, S.211, G.215, L.218, I.219, R.222 Ligands: LI1.49 Ligand excluded by PLIP LI1.49: 6 residues within 4Å: Chain C: Y.23, V.210, V.214, G.215, L.218 Ligands: LI1.48 Ligand excluded by PLIP LI1.50: 5 residues within 4Å: Chain C: I.8, A.11, L.12, A.15 Ligands: LI1.51 Ligand excluded by PLIP LI1.51: 5 residues within 4Å: Chain C: L.12, L.16, V.207, V.210 Ligands: LI1.50 Ligand excluded by PLIP LI1.52: 8 residues within 4Å: Chain A: L.25, M.29 Chain C: L.143, Y.144, L.146, Y.147, F.150, F.151 Ligand excluded by PLIP LI1.53: 3 residues within 4Å: Chain C: L.22, Y.23, V.26 Ligand excluded by PLIP

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

OLC.7: 22 residues within 4Å: Chain A: G.18, T.21, L.22, L.25, K.37, Y.40, A.41, T.44, L.45, A.48, F.51, T.52 Chain C: G.103, T.104, A.107, A.111, I.114, I.137, A.141, Y.144 Ligands: LI1.3, LI1.38 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.22, A:L.25, A:T.44, A:L.45, A:F.51, A:F.51, A:F.51, C:A.107, C:Y.144 Hydrogen bonds: A:K.37 OLC.8: 24 residues within 4Å: Chain A: L.45, I.49, T.52, M.53, Y.61, T.64, W.77, A.81, F.85, L.89 Chain C: L.106, V.109, G.110, G.113, I.114, G.117, T.118, L.120, V.121, L.124 Ligands: LI1.4, OLC.10, LI1.22, OLC.46 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.77, A:F.85, C:L.106 Water bridges: A:W.77 OLC.9: 4 residues within 4Å: Chain A: I.200, L.203, L.204, V.207 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.203 OLC.10: 18 residues within 4Å: Chain A: L.84, F.85, P.88, L.89, L.92, L.96, A.100, Q.102, I.105, L.106, V.109, G.113 Chain B: F.85 Chain C: Q.102 Ligands: OLC.8, OLC.26, OLC.28, OLC.46 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.84, A:P.88, A:P.88, A:L.96, A:I.105, A:V.109 Hydrogen bonds: C:Q.102 OLC.11: 13 residues within 4Å: Chain A: W.135, T.139, M.142, L.143, L.146, S.180, P.183, V.184, L.187, I.188, A.193, I.195 Ligands: LI1.6 No protein-ligand interaction detected (PLIP) OLC.25: 22 residues within 4Å: Chain A: G.103, T.104, A.107, A.111, I.114, I.137, A.141, Y.144 Chain B: G.18, T.21, L.22, L.25, K.37, Y.40, A.41, T.44, L.45, A.48, F.51, T.52 Ligands: LI1.2, LI1.21 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.22, B:L.25, B:T.44, B:L.45, B:F.51, B:F.51, B:F.51, A:A.107, A:Y.144 Hydrogen bonds: B:K.37 OLC.26: 24 residues within 4Å: Chain A: L.106, V.109, G.110, G.113, I.114, G.117, T.118, L.120, V.121, L.124 Chain B: L.45, I.49, T.52, M.53, Y.61, T.64, W.77, A.81, F.85, L.89 Ligands: OLC.10, LI1.22, OLC.28, LI1.40 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.106, B:W.77, B:F.85 Water bridges: B:W.77 OLC.27: 4 residues within 4Å: Chain B: I.200, L.203, L.204, V.207 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.203 OLC.28: 18 residues within 4Å: Chain A: Q.102 Chain B: L.84, F.85, P.88, L.89, L.92, L.96, A.100, Q.102, I.105, L.106, V.109, G.113 Chain C: F.85 Ligands: OLC.10, OLC.26, OLC.44, OLC.46 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.84, B:P.88, B:P.88, B:L.96, B:I.105, B:V.109 Hydrogen bonds: A:Q.102 OLC.29: 13 residues within 4Å: Chain B: W.135, T.139, M.142, L.143, L.146, S.180, P.183, V.184, L.187, I.188, A.193, I.195 Ligands: LI1.24 No protein-ligand interaction detected (PLIP) OLC.43: 22 residues within 4Å: Chain B: G.103, T.104, A.107, A.111, I.114, I.137, A.141, Y.144 Chain C: G.18, T.21, L.22, L.25, K.37, Y.40, A.41, T.44, L.45, A.48, F.51, T.52 Ligands: LI1.20, LI1.39 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.22, C:L.25, C:T.44, C:L.45, C:F.51, C:F.51, C:F.51, B:A.107, B:Y.144 Hydrogen bonds: C:K.37 OLC.44: 24 residues within 4Å: Chain B: L.106, V.109, G.110, G.113, I.114, G.117, T.118, L.120, V.121, L.124 Chain C: L.45, I.49, T.52, M.53, Y.61, T.64, W.77, A.81, F.85, L.89 Ligands: LI1.4, OLC.28, LI1.40, OLC.46 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.77, C:F.85, B:L.106 Water bridges: C:W.77 OLC.45: 4 residues within 4Å: Chain C: I.200, L.203, L.204, V.207 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.203 OLC.46: 18 residues within 4Å: Chain A: F.85 Chain B: Q.102 Chain C: L.84, F.85, P.88, L.89, L.92, L.96, A.100, Q.102, I.105, L.106, V.109, G.113 Ligands: OLC.8, OLC.10, OLC.28, OLC.44 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.84, C:P.88, C:P.88, C:L.96, C:I.105, C:V.109 Hydrogen bonds: B:Q.102 OLC.47: 13 residues within 4Å: Chain C: W.135, T.139, M.142, L.143, L.146, S.180, P.183, V.184, L.187, I.188, A.193, I.195 Ligands: LI1.42 No protein-ligand interaction detected (PLIP)

3 x RET: RETINAL(Covalent)

RET.18: 19 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, W.179, Y.182, P.183, W.186, D.209, A.212, K.213 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.87, A:M.142, A:W.179, A:Y.182, A:Y.182, A:Y.182, A:P.183, A:W.186, A:A.212, A:K.213 RET.36: 19 residues within 4Å: Chain B: Y.80, W.83, T.86, T.87, L.90, M.115, I.116, G.119, W.135, S.138, T.139, M.142, W.179, Y.182, P.183, W.186, D.209, A.212, K.213 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.87, B:M.142, B:W.179, B:Y.182, B:Y.182, B:Y.182, B:P.183, B:W.186, B:A.212, B:K.213 RET.54: 19 residues within 4Å: Chain C: Y.80, W.83, T.86, T.87, L.90, M.115, I.116, G.119, W.135, S.138, T.139, M.142, W.179, Y.182, P.183, W.186, D.209, A.212, K.213 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.87, C:M.142, C:W.179, C:Y.182, C:Y.182, C:Y.182, C:P.183, C:W.186, C:A.212, C: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: 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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Bacteriorhodopsin

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