SMTL ID : 1brr.1

X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

2 x GLC- MAN- SGA: 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose

GLC-MAN-SGA.1: 9 residues within 4Å: Chain A: Y.64, L.66, T.67 Chain B: T.67, L.127, K.129 Ligands: ARC.5, GOL.7, ARC.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.67, A:Y.64, A:T.67, A:T.67 GLC-MAN-SGA.2: 10 residues within 4Å: Chain A: T.67, P.70, L.127 Chain C: Y.64, L.66, T.67, W.80 Ligands: ARC.5, ARC.19, GOL.20 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:T.67, C:T.67, C:T.67, C:W.80

3 x RET: RETINAL(Covalent)

RET.3: 16 residues within 4Å: Chain A: W.86, T.89, T.90, L.93, M.118, I.119, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, K.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.89, A:T.90, A:L.93, A:I.119, A:M.145, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:K.216 RET.9: 17 residues within 4Å: Chain B: 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, K.216 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.89, B:T.90, B:L.93, B:I.119, B:M.145, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:K.216 RET.16: 17 residues within 4Å: Chain C: 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, K.216 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:T.89, C:T.90, C:L.93, C:I.119, C:M.145, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:K.216

10 x ARC: 3,7,11,15-TETRAMETHYL-HEXADECAN-1-OL(Non-covalent)

ARC.4: 13 residues within 4Å: Chain A: G.106, T.107, A.110, A.114, A.143, Y.147 Chain C: L.28, G.31, K.40, Y.43, A.44, T.47, L.48 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.28, C:Y.43, C:T.47, C:L.48, A:A.110, A:A.114, A:Y.147, A:Y.147, A:Y.147 ARC.5: 10 residues within 4Å: Chain A: Y.64, W.80, L.123 Ligands: GLC-MAN-SGA.1, GLC-MAN-SGA.2, GOL.7, ARC.12, ARC.13, ARC.19, GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.80, A:L.123 ARC.6: 13 residues within 4Å: Chain A: V.112, G.113, G.116, I.117, G.120, V.124 Chain C: T.55, M.56, Y.64, W.80, F.88 Ligands: ARC.19, GOL.20 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:T.55, C:W.80, C:F.88, C:F.88, A:V.112, A:I.117, A:V.124 Hydrogen bonds: C:Y.64 ARC.10: 12 residues within 4Å: Chain A: F.27, L.28, Y.43, A.44, T.47 Chain B: G.106, T.107, A.110, A.114, A.143, A.144, Y.147 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.110, B:A.114, B:Y.147, A:L.28, A:Y.43 Hydrogen bonds: B:G.106 ARC.11: 15 residues within 4Å: Chain B: T.55, M.56, Y.64, W.80, A.84, F.88, L.92 Chain C: G.113, G.116, I.117, G.120, L.123, V.124 Ligands: ARC.12, GOL.15 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.55, B:W.80, B:A.84, B:F.88, B:F.88, B:F.88, B:L.92, C:V.124 ARC.12: 8 residues within 4Å: Chain B: F.88, L.123 Ligands: GLC-MAN-SGA.1, ARC.5, GOL.7, ARC.11, GOL.15, ARC.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.88, B:F.88, B:F.88 ARC.13: 11 residues within 4Å: Chain A: T.55, M.56, Y.64, W.80, F.88 Chain B: G.113, G.116, G.120, L.123 Ligands: ARC.5, GOL.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.55, A:W.80, A:F.88, A:F.88, A:F.88, B:L.123 ARC.17: 6 residues within 4Å: Chain C: V.180, L.181, S.183, A.184, L.207, L.211 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.180, C:L.181, C:A.184, C:L.207, C:L.211 ARC.18: 12 residues within 4Å: Chain B: F.27, L.28, G.31, K.40, Y.43, A.44, T.47, L.48 Chain C: G.106, T.107, A.110, Y.147 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.28, B:L.28, B:Y.43, B:T.47, B:L.48, C:A.110 Hydrogen bonds: C:G.106 ARC.19: 10 residues within 4Å: Chain A: L.87 Chain C: W.80, L.87, F.88, L.123 Ligands: GLC-MAN-SGA.2, ARC.5, ARC.6, ARC.12, GOL.20 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.80, C:W.80, C:W.80, C:L.87, C:L.123, A:L.87, A:L.87

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.64 Chain B: L.127 Ligands: GLC-MAN-SGA.1, ARC.5, ARC.12, ARC.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.127 GOL.15: 3 residues within 4Å: Chain B: Y.64 Ligands: ARC.11, ARC.12 No protein-ligand interaction detected (PLIP) GOL.20: 6 residues within 4Å: Chain A: L.127 Chain C: Y.64 Ligands: GLC-MAN-SGA.2, ARC.5, ARC.6, ARC.19 No protein-ligand interaction detected (PLIP)

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.8: 4 residues within 4Å: Chain B: L.15, A.18, L.22 Ligands: OCT.14 No protein-ligand interaction detected (PLIP)

1 x OCT: N-OCTANE(Non-functional Binders)

OCT.14: 1 residues within 4Å: Ligands: BGC.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Essen, L. et al., Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex. Proc.Natl.Acad.Sci.USA (1998)

Release Date

1998-09-30

Peptides

PROTEIN (BACTERIORHODOPSIN): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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PROTEIN (BACTERIORHODOPSIN)