SMTL ID : 1x0s.1

Crystal structure of the 13-cis isomer of bacteriorhodopsin

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: 9 residues within 4Å: Chain A: T.67, M.68, K.129 Chain B: Y.64, L.66, T.67, W.80 Ligands: SO4.2, L2P.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.67, A:K.129, B:L.66, B:T.67, B:W.80 Water bridges: A:T.67, B:T.67 GLC-MAN-GAL.9: 9 residues within 4Å: Chain B: T.67, M.68, K.129 Chain C: Y.64, L.66, T.67, W.80 Ligands: SO4.10, L2P.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.67, B:K.129, C:L.66, C:T.67, C:W.80 Water bridges: B:T.67, C:T.67 GLC-MAN-GAL.17: 9 residues within 4Å: Chain A: Y.64, L.66, T.67, W.80 Chain C: T.67, M.68, K.129 Ligands: SO4.18, L2P.21 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:T.67, C:T.67 Hydrogen bonds: C:T.67, A:L.66, A:T.67, A:W.80, C:K.129

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: T.128, K.129, V.130 Chain B: L.62, G.63, Y.64 Ligands: GLC-MAN-GAL.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.129, A:V.130 Salt bridges: A:K.129 Water bridges: B:Y.64, B:Y.64 SO4.10: 7 residues within 4Å: Chain B: T.128, K.129, V.130 Chain C: L.62, G.63, Y.64 Ligands: GLC-MAN-GAL.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.129, B:V.130 Salt bridges: B:K.129 Water bridges: C:Y.64, C:Y.64 SO4.18: 7 residues within 4Å: Chain A: L.62, G.63, Y.64 Chain C: T.128, K.129, V.130 Ligands: GLC-MAN-GAL.17 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.129, C:V.130 Salt bridges: C:K.129 Water bridges: A:Y.64, A:Y.64

3 x RET: RETINAL(Covalent)

RET.3: 17 residues within 4Å: Chain A: Y.83, W.86, T.90, L.93, M.118, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.83, A:T.90, A:L.93, A:M.145, A:W.182, A:W.182, A:Y.185, 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, A:K.216 RET.11: 17 residues within 4Å: Chain B: Y.83, W.86, T.90, L.93, M.118, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.83, B:T.90, B:L.93, B:M.145, B:W.182, B:W.182, B:Y.185, 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, B:K.216 RET.19: 17 residues within 4Å: Chain C: Y.83, W.86, T.90, L.93, M.118, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.83, C:T.90, C:L.93, C:M.145, C:W.182, 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:W.189, C:A.215, C:K.216, C:K.216

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

L3P.4: 24 residues within 4Å: Chain A: G.21, L.25, L.28, V.29, M.32, S.35, P.37, K.40, A.44, T.47, L.48, A.51, F.54 Chain C: D.104, T.107, A.110, I.117, I.140, A.143, A.144, Y.147, Y.150 Ligands: L3P.6, L3P.8 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:L.25, A:V.29, A:T.47, A:L.48, A:L.48, A:A.51, A:F.54, A:F.54, C:I.117, C:I.140, C:A.143, C:A.144, C:Y.147, C:Y.150 Hydrogen bonds: A:S.35 Water bridges: A:T.47 Salt bridges: A:K.40, A:K.40, C:K.159 L3P.6: 10 residues within 4Å: Chain A: R.7, W.10, F.54, L.61, L.62 Chain C: Y.133, V.136, I.140 Ligands: L3P.4, L3P.23 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.136, C:V.136, C:I.140, A:F.54, A:L.61 Salt bridges: A:R.7 L3P.7: 8 residues within 4Å: Chain A: Y.131, F.135, W.138, A.139, L.190, A.196, I.198 Ligands: L3P.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.138, A:A.139, A:L.190, A:A.196 Hydrogen bonds: A:Y.131 L3P.8: 5 residues within 4Å: Chain C: A.143, L.146, Y.150, F.154 Ligands: L3P.4 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.143, C:L.146, C:L.146, C:Y.150 L3P.12: 24 residues within 4Å: Chain A: D.104, T.107, A.110, I.117, I.140, A.143, A.144, Y.147, Y.150 Chain B: G.21, L.25, L.28, V.29, M.32, S.35, P.37, K.40, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.14, L3P.16 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.25, B:V.29, B:T.47, B:L.48, B:L.48, B:A.51, B:F.54, B:F.54, A:I.117, A:I.140, A:A.143, A:A.144, A:Y.147, A:Y.150 Hydrogen bonds: B:S.35 Water bridges: B:T.47 Salt bridges: B:K.40, B:K.40, A:K.159 L3P.14: 10 residues within 4Å: Chain A: Y.133, V.136, I.140 Chain B: R.7, W.10, F.54, L.61, L.62 Ligands: L3P.7, L3P.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.136, A:V.136, A:I.140, B:F.54, B:L.61 Salt bridges: B:R.7 L3P.15: 8 residues within 4Å: Chain B: Y.131, F.135, W.138, A.139, L.190, A.196, I.198 Ligands: L3P.22 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.138, B:A.139, B:L.190, B:A.196 Hydrogen bonds: B:Y.131 L3P.16: 5 residues within 4Å: Chain A: A.143, L.146, Y.150, F.154 Ligands: L3P.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.143, A:L.146, A:L.146, A:Y.150 L3P.20: 24 residues within 4Å: Chain B: D.104, T.107, A.110, I.117, I.140, A.143, A.144, Y.147, Y.150 Chain C: G.21, L.25, L.28, V.29, M.32, S.35, P.37, K.40, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.22, L3P.24 19 PLIP interactions: 12 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:L.25, C:V.29, C:T.47, C:L.48, C:L.48, C:A.51, C:F.54, C:F.54, B:I.117, B:I.140, B:A.143, B:A.144, B:Y.147, B:Y.150 Hydrogen bonds: C:S.35 Water bridges: C:T.47 Salt bridges: C:K.40, C:K.40, B:K.159 L3P.22: 10 residues within 4Å: Chain B: Y.133, V.136, I.140 Chain C: R.7, W.10, F.54, L.61, L.62 Ligands: L3P.15, L3P.20 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.54, C:L.61, B:V.136, B:V.136, B:I.140 Salt bridges: C:R.7 L3P.23: 8 residues within 4Å: Chain C: Y.131, F.135, W.138, A.139, L.190, A.196, I.198 Ligands: L3P.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.138, C:A.139, C:L.190, C:A.196 Hydrogen bonds: C:Y.131 L3P.24: 5 residues within 4Å: Chain B: A.143, L.146, Y.150, F.154 Ligands: L3P.20 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.143, B:L.146, B:L.146, B:Y.150

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

L2P.5: 20 residues within 4Å: Chain A: L.87, F.88, G.113, G.116, G.120, L.123 Chain B: I.52, M.56, Y.64, W.80, Y.83, A.84, L.87, F.88, L.123, L.127 Ligands: GLC-MAN-GAL.1, GLC-MAN-GAL.1, L2P.13, L2P.21 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.52, B:W.80, B:W.80, B:W.80, B:W.80, B:A.84, B:L.87, B:F.88, B:F.88, B:F.88, B:F.88, B:L.123, B:L.127, A:L.87, A:L.87, A:F.88, A:L.123 L2P.13: 20 residues within 4Å: Chain B: L.87, F.88, G.113, G.116, G.120, L.123 Chain C: I.52, M.56, Y.64, W.80, Y.83, A.84, L.87, F.88, L.123, L.127 Ligands: L2P.5, GLC-MAN-GAL.9, GLC-MAN-GAL.9, L2P.21 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.52, C:W.80, C:W.80, C:W.80, C:W.80, C:A.84, C:L.87, C:F.88, C:F.88, C:F.88, C:F.88, C:L.123, C:L.127, B:L.87, B:L.87, B:F.88, B:L.123 L2P.21: 20 residues within 4Å: Chain A: I.52, M.56, Y.64, W.80, Y.83, A.84, L.87, F.88, L.123, L.127 Chain C: L.87, F.88, G.113, G.116, G.120, L.123 Ligands: L2P.5, L2P.13, GLC-MAN-GAL.17, GLC-MAN-GAL.17 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.52, A:W.80, A:W.80, A:W.80, A:W.80, A:A.84, A:L.87, A:F.88, A:F.88, A:F.88, A:F.88, A:L.123, A:L.127, C:L.87, C:L.87, C:F.88, C:L.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishikawa, T. et al., Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state. J.Mol.Biol. (2005)

Release Date

2005-08-30

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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