SMTL ID : 5j7a.1

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.82, A:T.86, A:W.178, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:W.185, A:A.211, A:K.212 RET.7: 16 residues within 4Å: Chain B: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.82, B:T.86, B:W.178, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:P.182, B:W.185, B:A.211, B:K.212 RET.13: 16 residues within 4Å: Chain C: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.82, C:T.86, C:W.178, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:P.182, C:W.185, C:A.211, C:K.212

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

LI1.2: 2 residues within 4Å: Chain A: F.131, A.135 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.131, A:A.135 LI1.3: 11 residues within 4Å: Chain A: G.17, T.20, L.24, K.36, Y.39, A.40, T.43, F.50 Chain C: A.106, Y.143 Ligands: LI1.17 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.143, A:T.20, A:T.43, A:F.50 LI1.4: 2 residues within 4Å: Chain A: Y.60, W.76 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.76 LI1.5: 6 residues within 4Å: Chain A: V.132, A.135, A.139 Chain B: L.54, L.58 Ligands: LI1.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.54, B:L.58, A:V.132, A:A.139 LI1.6: 3 residues within 4Å: Chain A: I.48 Chain C: G.112, I.113 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.48 LI1.8: 2 residues within 4Å: Chain B: F.131, A.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.131, B:A.135 LI1.9: 11 residues within 4Å: Chain A: A.106, Y.143 Chain B: G.17, T.20, L.24, K.36, Y.39, A.40, T.43, F.50 Ligands: LI1.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.20, B:T.43, B:F.50, A:Y.143 LI1.10: 2 residues within 4Å: Chain B: Y.60, W.76 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.76 LI1.11: 6 residues within 4Å: Chain B: V.132, A.135, A.139 Chain C: L.54, L.58 Ligands: LI1.15 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.54, C:L.58, B:V.132, B:A.139 LI1.12: 3 residues within 4Å: Chain A: G.112, I.113 Chain B: I.48 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.48 LI1.14: 2 residues within 4Å: Chain C: F.131, A.135 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.131, C:A.135 LI1.15: 11 residues within 4Å: Chain B: A.106, Y.143 Chain C: G.17, T.20, L.24, K.36, Y.39, A.40, T.43, F.50 Ligands: LI1.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.20, C:T.43, C:F.50, B:Y.143 LI1.16: 2 residues within 4Å: Chain C: Y.60, W.76 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.76 LI1.17: 6 residues within 4Å: Chain A: L.54, L.58 Chain C: V.132, A.135, A.139 Ligands: LI1.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.54, A:L.58, C:V.132, C:A.139 LI1.18: 3 residues within 4Å: Chain B: G.112, I.113 Chain C: I.48 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogly, P. et al., Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat Commun (2016)

Release Date

2016-08-31

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