SMTL ID : 4x31.1

Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: W.82, T.85, T.86, L.89, M.114, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, K.212 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.82, A:T.86, A:L.89, A:M.141, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:W.185, A:K.212 RET.7: 15 residues within 4Å: Chain B: W.82, T.85, T.86, L.89, M.114, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, K.212 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.82, B:T.86, B:L.89, B:M.141, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:P.182, B:W.185, B:K.212 RET.13: 15 residues within 4Å: Chain C: W.82, T.85, T.86, L.89, M.114, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, K.212 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.82, C:T.86, C:L.89, C:M.141, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:P.182, C:W.185, 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: 10 residues within 4Å: Chain A: G.17, T.20, L.24, Y.39, A.40, T.43, L.44, F.50 Chain C: A.106, Y.143 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:T.20, A:L.24, A:T.43, A:L.44, A:F.50, A:F.50, C:A.106 LI1.3: 8 residues within 4Å: Chain A: I.48, M.52, Y.60, W.76 Chain C: G.112, I.113, G.116, L.119 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.113, C:L.119, A:I.48, A:W.76 LI1.4: 2 residues within 4Å: Chain A: T.63, W.76 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.63, A:W.76, A:W.76 LI1.5: 1 residues within 4Å: Chain A: F.131 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.131 LI1.6: 3 residues within 4Å: Chain A: Y.129, I.136 Chain B: L.54 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.54, A:Y.129, A:I.136 LI1.8: 10 residues within 4Å: Chain A: A.106, Y.143 Chain B: G.17, T.20, L.24, Y.39, A.40, T.43, L.44, F.50 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.20, B:L.24, B:T.43, B:L.44, B:F.50, B:F.50, A:A.106 LI1.9: 8 residues within 4Å: Chain A: G.112, I.113, G.116, L.119 Chain B: I.48, M.52, Y.60, W.76 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.113, A:L.119, B:I.48, B:W.76 LI1.10: 2 residues within 4Å: Chain B: T.63, W.76 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.63, B:W.76, B:W.76 LI1.11: 1 residues within 4Å: Chain B: F.131 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.131 LI1.12: 3 residues within 4Å: Chain B: Y.129, I.136 Chain C: L.54 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.54, B:Y.129, B:I.136 LI1.14: 10 residues within 4Å: Chain B: A.106, Y.143 Chain C: G.17, T.20, L.24, Y.39, A.40, T.43, L.44, F.50 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.20, C:L.24, C:T.43, C:L.44, C:F.50, C:F.50, B:A.106 LI1.15: 8 residues within 4Å: Chain B: G.112, I.113, G.116, L.119 Chain C: I.48, M.52, Y.60, W.76 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.113, B:L.119, C:I.48, C:W.76 LI1.16: 2 residues within 4Å: Chain C: T.63, W.76 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.63, C:W.76, C:W.76 LI1.17: 1 residues within 4Å: Chain C: F.131 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.131 LI1.18: 3 residues within 4Å: Chain A: L.54 Chain C: Y.129, I.136 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.54, C:Y.129, C:I.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogly, P. et al., Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. Iucrj (2015)

Release Date

2015-02-18

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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