SMTL ID : 1qm8.1

Structure of Bacteriorhodopsin at 100 K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

GLC-MAN-GAL.1: 10 residues within 4Å: Chain A: T.67, V.69, L.127, K.129 Chain C: Y.64, L.66, T.67, W.80 Ligands: L2P.4, L2P.11 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:L.66, A:T.67, A:K.129, A:K.129, C:T.67, C:W.80 GLC-MAN-GAL.8: 10 residues within 4Å: Chain A: Y.64, L.66, T.67, W.80 Chain B: T.67, V.69, L.127, K.129 Ligands: L2P.11, L2P.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.66, B:T.67, B:K.129, B:K.129, A:T.67, A:W.80 GLC-MAN-GAL.15: 10 residues within 4Å: Chain B: Y.64, L.66, T.67, W.80 Chain C: T.67, V.69, L.127, K.129 Ligands: L2P.4, L2P.18 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:L.66, C:T.67, B:T.67, B:W.80, C:K.129, C:K.129

3 x RET: RETINAL(Covalent)

RET.2: 17 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.83, A:W.86, A:W.86, A:T.89, A:T.90, A:L.93, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:W.189, A:A.215, A:K.216 RET.9: 17 residues within 4Å: Chain B: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.83, B:W.86, B:W.86, B:T.89, B:T.90, B:L.93, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:W.189, B:A.215, B:K.216 RET.16: 17 residues within 4Å: Chain C: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Y.83, C:W.86, C:W.86, C:T.89, C:T.90, C:L.93, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:W.189, C:A.215, C:K.216

3 x L1P: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L1P.3: 17 residues within 4Å: Chain A: L.28, K.40, A.44, T.47, L.48, A.51, F.54 Chain B: T.107, A.110, A.114, I.117, I.140, A.144, L.146, Y.147, Y.150 Ligands: L3P.5 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.28, A:A.44, A:L.48, A:A.51, A:F.54, B:A.110, B:A.114, B:I.117, B:I.140, B:L.146, B:L.146, B:Y.147, B:Y.147, B:Y.150, B:Y.150 Salt bridges: A:K.40 Hydrogen bonds: B:T.107 L1P.10: 17 residues within 4Å: Chain B: L.28, K.40, A.44, T.47, L.48, A.51, F.54 Chain C: T.107, A.110, A.114, I.117, I.140, A.144, L.146, Y.147, Y.150 Ligands: L3P.12 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:L.28, B:A.44, B:L.48, B:A.51, B:F.54, C:A.110, C:A.114, C:I.117, C:I.140, C:L.146, C:L.146, C:Y.147, C:Y.147, C:Y.150, C:Y.150 Salt bridges: B:K.40 Hydrogen bonds: C:T.107 L1P.17: 17 residues within 4Å: Chain A: T.107, A.110, A.114, I.117, I.140, A.144, L.146, Y.147, Y.150 Chain C: L.28, K.40, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.19 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain A Hydrophobic interactions: C:L.28, C:A.44, C:L.48, C:A.51, C:F.54, A:A.110, A:A.114, A:I.117, A:I.140, A:L.146, A:L.146, A:Y.147, A:Y.147, A:Y.150, A:Y.150 Salt bridges: C:K.40 Hydrogen bonds: A:T.107

6 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)

L2P.4: 22 residues within 4Å: Chain A: L.109, G.113, G.116, I.117, G.120, T.121, V.124, L.127 Chain C: L.48, I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.92, L.123, L.127 Ligands: GLC-MAN-GAL.1, GLC-MAN-GAL.1, GLC-MAN-GAL.15 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.109, A:I.117, A:V.124, C:L.48, C:I.52, C:W.80, C:W.80, C:A.84, C:L.87, C:F.88, C:L.92, C:L.123, C:L.127 L2P.7: 5 residues within 4Å: Chain A: L.19, Y.26, V.29, L.221, R.225 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.19, A:Y.26, A:Y.26, A:L.221 L2P.11: 22 residues within 4Å: Chain A: L.48, I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.92, L.123, L.127 Chain B: L.109, G.113, G.116, I.117, G.120, T.121, V.124, L.127 Ligands: GLC-MAN-GAL.1, GLC-MAN-GAL.8, GLC-MAN-GAL.8 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.48, A:I.52, A:W.80, A:W.80, A:A.84, A:L.87, A:F.88, A:L.92, A:L.123, A:L.127, B:L.109, B:I.117, B:V.124 L2P.14: 5 residues within 4Å: Chain B: L.19, Y.26, V.29, L.221, R.225 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.19, B:Y.26, B:Y.26, B:L.221 L2P.18: 22 residues within 4Å: Chain B: L.48, I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.92, L.123, L.127 Chain C: L.109, G.113, G.116, I.117, G.120, T.121, V.124, L.127 Ligands: GLC-MAN-GAL.8, GLC-MAN-GAL.15, GLC-MAN-GAL.15 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.48, B:I.52, B:W.80, B:W.80, B:A.84, B:L.87, B:F.88, B:L.92, B:L.123, B:L.127, C:L.109, C:I.117, C:V.124 L2P.21: 5 residues within 4Å: Chain C: L.19, Y.26, V.29, L.221, R.225 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.19, C:Y.26, C:Y.26, C:L.221

3 x L3P: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE(Non-covalent)

L3P.5: 13 residues within 4Å: Chain A: G.6, W.10, A.14, T.17, A.18, M.60, L.61, L.62, G.63 Chain B: Y.133, A.139, A.143 Ligands: L1P.3 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.143, A:T.17, A:A.18 Hydrogen bonds: B:Y.133, B:Y.133, A:G.6 Water bridges: A:R.7 L3P.12: 13 residues within 4Å: Chain B: G.6, W.10, A.14, T.17, A.18, M.60, L.61, L.62, G.63 Chain C: Y.133, A.139, A.143 Ligands: L1P.10 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.143, B:T.17, B:A.18 Hydrogen bonds: C:Y.133, C:Y.133, B:G.6 Water bridges: B:R.7 L3P.19: 13 residues within 4Å: Chain A: Y.133, A.139, A.143 Chain C: G.6, W.10, A.14, T.17, A.18, M.60, L.61, L.62, G.63 Ligands: L1P.17 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:T.17, C:A.18, A:A.143 Hydrogen bonds: C:G.6, A:Y.133, A:Y.133 Water bridges: C:R.7

3 x L4P: 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L4P.6: 7 residues within 4Å: Chain A: Y.131, S.132, F.135, W.138, A.139, L.190, A.196 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.135, A:A.139, A:L.190 Hydrogen bonds: A:Y.131 L4P.13: 7 residues within 4Å: Chain B: Y.131, S.132, F.135, W.138, A.139, L.190, A.196 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.135, B:A.139, B:L.190 Hydrogen bonds: B:Y.131 L4P.20: 7 residues within 4Å: Chain C: Y.131, S.132, F.135, W.138, A.139, L.190, A.196 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.135, C:A.139, C:L.190 Hydrogen bonds: C:Y.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeda, K. et al., A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies. J.Mol.Biol. (1998)

Release Date

2000-08-16

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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