SMTL ID : 6g7i.1

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 49-406 fs state structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 18 residues within 4Å: Chain A: Y.96, W.99, T.103, L.106, M.131, I.132, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.99, A:T.103, A:W.195, A:Y.198, A:Y.198, A:Y.198, A:Y.198, A:W.202, A:A.228, A:K.229 RET.13: 18 residues within 4Å: Chain B: Y.96, W.99, T.103, L.106, M.131, I.132, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.99, B:T.103, B:W.195, B:Y.198, B:Y.198, B:Y.198, B:Y.198, B:W.202, B:A.228, B:K.229 RET.25: 18 residues within 4Å: Chain C: Y.96, W.99, T.103, L.106, M.131, I.132, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.99, C:T.103, C:W.195, C:Y.198, C:Y.198, C:Y.198, C:Y.198, C:W.202, C:A.228, C:K.229

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

LI1.2: 3 residues within 4Å: Chain A: F.148, V.149, A.152 Ligand excluded by PLIP LI1.3: 9 residues within 4Å: Chain A: Y.146, V.149, I.153 Chain B: F.67, L.71, L.75 Ligands: LI1.4, LI1.17, OLC.21 Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Ligands: LI1.3, LI1.17, OLC.21 Ligand excluded by PLIP LI1.5: 10 residues within 4Å: Chain A: A.27, T.30, A.31, G.34, L.35, F.67, L.74 Ligands: OLC.9, LI1.27, LI1.28 Ligand excluded by PLIP LI1.6: 9 residues within 4Å: Chain C: W.93, A.97, L.100, L.136, L.140 Ligands: OLC.10, LI1.18, LI1.30, OLC.34 Ligand excluded by PLIP LI1.7: 1 residues within 4Å: Chain A: F.167 Ligand excluded by PLIP LI1.8: 7 residues within 4Å: Chain A: F.166, N.189, V.192, V.193, S.196, A.197 Ligands: OLC.11 Ligand excluded by PLIP LI1.14: 3 residues within 4Å: Chain B: F.148, V.149, A.152 Ligand excluded by PLIP LI1.15: 9 residues within 4Å: Chain B: Y.146, V.149, I.153 Chain C: F.67, L.71, L.75 Ligands: LI1.16, LI1.29, OLC.33 Ligand excluded by PLIP LI1.16: 3 residues within 4Å: Ligands: LI1.15, LI1.29, OLC.33 Ligand excluded by PLIP LI1.17: 10 residues within 4Å: Chain B: A.27, T.30, A.31, G.34, L.35, F.67, L.74 Ligands: LI1.3, LI1.4, OLC.21 Ligand excluded by PLIP LI1.18: 9 residues within 4Å: Chain A: W.93, A.97, L.100, L.136, L.140 Ligands: LI1.6, OLC.10, OLC.22, LI1.30 Ligand excluded by PLIP LI1.19: 1 residues within 4Å: Chain B: F.167 Ligand excluded by PLIP LI1.20: 7 residues within 4Å: Chain B: F.166, N.189, V.192, V.193, S.196, A.197 Ligands: OLC.23 Ligand excluded by PLIP LI1.26: 3 residues within 4Å: Chain C: F.148, V.149, A.152 Ligand excluded by PLIP LI1.27: 9 residues within 4Å: Chain A: F.67, L.71, L.75 Chain C: Y.146, V.149, I.153 Ligands: LI1.5, OLC.9, LI1.28 Ligand excluded by PLIP LI1.28: 3 residues within 4Å: Ligands: LI1.5, OLC.9, LI1.27 Ligand excluded by PLIP LI1.29: 10 residues within 4Å: Chain C: A.27, T.30, A.31, G.34, L.35, F.67, L.74 Ligands: LI1.15, LI1.16, OLC.33 Ligand excluded by PLIP LI1.30: 9 residues within 4Å: Chain B: W.93, A.97, L.100, L.136, L.140 Ligands: LI1.6, LI1.18, OLC.22, OLC.34 Ligand excluded by PLIP LI1.31: 1 residues within 4Å: Chain C: F.167 Ligand excluded by PLIP LI1.32: 7 residues within 4Å: Chain C: F.166, N.189, V.192, V.193, S.196, A.197 Ligands: OLC.35 Ligand excluded by PLIP

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

OLC.9: 24 residues within 4Å: Chain A: G.34, T.37, L.38, L.41, K.53, Y.56, A.57, T.60, L.61, A.64, F.67, T.68 Chain C: G.119, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160 Ligands: LI1.5, LI1.27, LI1.28 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.38, A:T.60, A:L.61, A:F.67, C:A.123, C:A.157, C:Y.160 Hydrogen bonds: A:K.53 Water bridges: A:G.44 OLC.10: 21 residues within 4Å: Chain A: L.61, I.65, T.68, M.69, Y.77, W.93, A.97, F.101, L.105 Chain C: L.122, V.125, G.126, G.129, I.130, G.133, T.134, L.136, V.137, L.140 Ligands: LI1.6, LI1.18 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.101, C:L.122, C:I.130, C:V.137 Water bridges: A:Y.77, A:W.93 OLC.11: 13 residues within 4Å: Chain A: W.151, T.155, M.158, L.159, L.162, S.196, P.199, V.200, L.203, I.204, A.209, I.211 Ligands: LI1.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.151 OLC.12: 4 residues within 4Å: Chain A: I.216, L.219, L.220, V.223 No protein-ligand interaction detected (PLIP) OLC.21: 24 residues within 4Å: Chain A: G.119, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160 Chain B: G.34, T.37, L.38, L.41, K.53, Y.56, A.57, T.60, L.61, A.64, F.67, T.68 Ligands: LI1.3, LI1.4, LI1.17 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.123, A:A.157, A:Y.160, B:L.38, B:T.60, B:L.61, B:F.67 Hydrogen bonds: B:K.53 Water bridges: B:G.44 OLC.22: 21 residues within 4Å: Chain A: L.122, V.125, G.126, G.129, I.130, G.133, T.134, L.136, V.137, L.140 Chain B: L.61, I.65, T.68, M.69, Y.77, W.93, A.97, F.101, L.105 Ligands: LI1.18, LI1.30 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.101, A:L.122, A:I.130, A:V.137 Water bridges: B:Y.77, B:W.93 OLC.23: 13 residues within 4Å: Chain B: W.151, T.155, M.158, L.159, L.162, S.196, P.199, V.200, L.203, I.204, A.209, I.211 Ligands: LI1.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.151 OLC.24: 4 residues within 4Å: Chain B: I.216, L.219, L.220, V.223 No protein-ligand interaction detected (PLIP) OLC.33: 24 residues within 4Å: Chain B: G.119, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160 Chain C: G.34, T.37, L.38, L.41, K.53, Y.56, A.57, T.60, L.61, A.64, F.67, T.68 Ligands: LI1.15, LI1.16, LI1.29 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.123, B:A.157, B:Y.160, C:L.38, C:T.60, C:L.61, C:F.67 Hydrogen bonds: C:K.53 Water bridges: C:G.44 OLC.34: 21 residues within 4Å: Chain B: L.122, V.125, G.126, G.129, I.130, G.133, T.134, L.136, V.137, L.140 Chain C: L.61, I.65, T.68, M.69, Y.77, W.93, A.97, F.101, L.105 Ligands: LI1.6, LI1.30 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.101, B:L.122, B:I.130, B:V.137 Water bridges: C:Y.77, C:W.93 OLC.35: 13 residues within 4Å: Chain C: W.151, T.155, M.158, L.159, L.162, S.196, P.199, V.200, L.203, I.204, A.209, I.211 Ligands: LI1.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.151 OLC.36: 4 residues within 4Å: Chain C: I.216, L.219, L.220, V.223 No protein-ligand interaction detected (PLIP)

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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