SMTL ID : 6g7h.1

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 19 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.90, A:L.93, A:M.145, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:A.215, A:K.216 RET.13: 19 residues within 4Å: Chain B: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.90, B:L.93, B:M.145, B:W.182, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:A.215, B:K.216 RET.25: 19 residues within 4Å: Chain C: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.90, C:L.93, C:M.145, C:W.182, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:A.215, C:K.216

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

LI1.2: 4 residues within 4Å: Chain A: S.132, F.135, V.136, A.139 Ligand excluded by PLIP LI1.3: 8 residues within 4Å: Chain A: Y.133, V.136, I.140 Chain B: F.54, L.58, L.62 Ligands: LI1.4, LI1.17 Ligand excluded by PLIP LI1.4: 1 residues within 4Å: Ligands: LI1.3 Ligand excluded by PLIP LI1.5: 8 residues within 4Å: Chain A: A.14, T.17, A.18, L.22, F.54, L.61 Ligands: OLC.9, LI1.27 Ligand excluded by PLIP LI1.6: 9 residues within 4Å: Chain C: T.67, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: OLC.10, OLC.34 Ligand excluded by PLIP LI1.7: 1 residues within 4Å: Chain A: F.154 Ligand excluded by PLIP LI1.8: 8 residues within 4Å: Chain A: F.153, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: OLC.11 Ligand excluded by PLIP LI1.14: 4 residues within 4Å: Chain B: S.132, F.135, V.136, A.139 Ligand excluded by PLIP LI1.15: 8 residues within 4Å: Chain B: Y.133, V.136, I.140 Chain C: F.54, L.58, L.62 Ligands: LI1.16, LI1.29 Ligand excluded by PLIP LI1.16: 1 residues within 4Å: Ligands: LI1.15 Ligand excluded by PLIP LI1.17: 8 residues within 4Å: Chain B: A.14, T.17, A.18, L.22, F.54, L.61 Ligands: LI1.3, OLC.21 Ligand excluded by PLIP LI1.18: 9 residues within 4Å: Chain A: T.67, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: OLC.10, OLC.22 Ligand excluded by PLIP LI1.19: 1 residues within 4Å: Chain B: F.154 Ligand excluded by PLIP LI1.20: 8 residues within 4Å: Chain B: F.153, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: OLC.23 Ligand excluded by PLIP LI1.26: 4 residues within 4Å: Chain C: S.132, F.135, V.136, A.139 Ligand excluded by PLIP LI1.27: 8 residues within 4Å: Chain A: F.54, L.58, L.62 Chain C: Y.133, V.136, I.140 Ligands: LI1.5, LI1.28 Ligand excluded by PLIP LI1.28: 1 residues within 4Å: Ligands: LI1.27 Ligand excluded by PLIP LI1.29: 8 residues within 4Å: Chain C: A.14, T.17, A.18, L.22, F.54, L.61 Ligands: LI1.15, OLC.33 Ligand excluded by PLIP LI1.30: 9 residues within 4Å: Chain B: T.67, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: OLC.22, OLC.34 Ligand excluded by PLIP LI1.31: 1 residues within 4Å: Chain C: F.154 Ligand excluded by PLIP LI1.32: 8 residues within 4Å: Chain C: F.153, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: OLC.35 Ligand excluded by PLIP

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

OLC.9: 21 residues within 4Å: Chain A: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Chain C: G.106, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147 Ligands: LI1.5 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.25, A:T.47, A:L.48, A:F.54, C:A.110, C:A.144, C:Y.147 Hydrogen bonds: A:K.40 OLC.10: 21 residues within 4Å: Chain A: L.48, I.52, T.55, M.56, Y.64, W.80, A.84, F.88, L.92 Chain C: L.109, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Ligands: LI1.6, LI1.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.109, C:I.117, A:F.88 Hydrogen bonds: A:W.80 OLC.11: 13 residues within 4Å: Chain A: W.138, T.142, M.145, L.146, L.149, S.183, P.186, V.187, L.190, I.191, A.196, I.198 Ligands: LI1.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.138, A:L.190 OLC.12: 4 residues within 4Å: Chain A: I.203, L.206, L.207, V.210 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.203 OLC.21: 21 residues within 4Å: Chain A: G.106, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147 Chain B: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: LI1.17 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.25, B:T.47, B:L.48, B:F.54, A:A.110, A:A.144, A:Y.147 Hydrogen bonds: B:K.40 OLC.22: 21 residues within 4Å: Chain A: L.109, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain B: L.48, I.52, T.55, M.56, Y.64, W.80, A.84, F.88, L.92 Ligands: LI1.18, LI1.30 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.109, A:I.117, B:F.88 Hydrogen bonds: B:W.80 OLC.23: 13 residues within 4Å: Chain B: W.138, T.142, M.145, L.146, L.149, S.183, P.186, V.187, L.190, I.191, A.196, I.198 Ligands: LI1.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.138, B:L.190 OLC.24: 4 residues within 4Å: Chain B: I.203, L.206, L.207, V.210 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.203 OLC.33: 21 residues within 4Å: Chain B: G.106, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147 Chain C: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: LI1.29 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.25, C:T.47, C:L.48, C:F.54, B:A.110, B:A.144, B:Y.147 Hydrogen bonds: C:K.40 OLC.34: 21 residues within 4Å: Chain B: L.109, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain C: L.48, I.52, T.55, M.56, Y.64, W.80, A.84, F.88, L.92 Ligands: LI1.6, LI1.30 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.109, B:I.117, C:F.88 Hydrogen bonds: C:W.80 OLC.35: 13 residues within 4Å: Chain C: W.138, T.142, M.145, L.146, L.149, S.183, P.186, V.187, L.190, I.191, A.196, I.198 Ligands: LI1.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.138, C:L.190 OLC.36: 4 residues within 4Å: Chain C: I.203, L.206, L.207, V.210 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogly, P. et al., Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science (2018)

Release Date

2018-06-27

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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