SMTL ID : 1ixf.1

Crystal Structure of the K intermediate of bacteriorhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: 8 residues within 4Å: Chain A: T.67, L.127, K.129 Chain B: Y.64, L.66, T.67, W.80 Ligands: L2P.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.67, B:L.66, B:T.67, B:W.80, A:K.129 Water bridges: A:T.67, B:M.68 GLC-MAN-GAL.8: 8 residues within 4Å: Chain B: T.67, L.127, K.129 Chain C: Y.64, L.66, T.67, W.80 Ligands: L2P.11 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.67, C:L.66, C:T.67, C:W.80, B:K.129 Water bridges: B:T.67, C:M.68 GLC-MAN-GAL.15: 8 residues within 4Å: Chain A: Y.64, L.66, T.67, W.80 Chain C: T.67, L.127, K.129 Ligands: L2P.18 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:T.67, A:L.66, A:T.67, A:W.80, C:K.129 Water bridges: C:T.67, A:M.68

3 x RET: RETINAL(Covalent)

RET.2: 14 residues within 4Å: Chain A: W.86, T.89, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, A.215, K.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.86, A:T.89, A:T.90, A:M.145, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:K.216 RET.9: 14 residues within 4Å: Chain B: W.86, T.89, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, A.215, K.216 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.86, B:T.89, B:T.90, B:M.145, B:W.182, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:K.216 RET.16: 14 residues within 4Å: Chain C: W.86, T.89, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, A.215, K.216 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.86, C:T.89, C:T.90, C:M.145, C:W.182, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:K.216

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

L3P.3: 26 residues within 4Å: Chain A: G.21, T.24, L.25, L.28, V.29, S.35, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Chain C: D.104, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147, Y.150, K.159 Ligands: L3P.5, L3P.7 23 PLIP interactions: 10 interactions with chain A, 13 interactions with chain C Hydrophobic interactions: A:L.25, A:L.28, A:V.29, A:T.47, A:L.48, A:L.48, A:A.51, A:F.54, C:A.110, C:A.114, C:I.117, C:I.117, C:A.143, C:A.144, C:Y.147, C:Y.147, C:Y.147, C:Y.150 Hydrogen bonds: A:S.35, C:D.104, C:Y.147 Salt bridges: A:K.40, C:K.159 L3P.5: 14 residues within 4Å: Chain A: R.7, W.10, A.14, T.17, A.18, F.54, L.61, L.62 Chain C: Y.133, V.136, I.140 Ligands: L3P.3, L3P.7, L3P.20 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.17, A:A.18, A:F.54, C:V.136, C:I.140 Salt bridges: A:R.7 Hydrogen bonds: C:Y.133 L3P.6: 9 residues within 4Å: Chain A: Y.131, F.135, A.139, V.187, L.190, G.197, I.198 Ligands: L3P.12, L3P.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.135, A:F.135, A:A.139, A:V.187, A:L.190, A:I.198, A:I.198 Hydrogen bonds: A:Y.131 L3P.7: 7 residues within 4Å: Chain C: A.143, L.146, Y.150, F.154 Ligands: L3P.3, L3P.5, L3P.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.143, C:L.146, C:Y.150 Hydrogen bonds: C:Y.150 L3P.10: 26 residues within 4Å: Chain A: D.104, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147, Y.150, K.159 Chain B: G.21, T.24, L.25, L.28, V.29, S.35, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.12, L3P.14 23 PLIP interactions: 13 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.110, A:A.114, A:I.117, A:I.117, A:A.143, A:A.144, A:Y.147, A:Y.147, A:Y.147, A:Y.150, B:L.25, B:L.28, B:V.29, B:T.47, B:L.48, B:L.48, B:A.51, B:F.54 Hydrogen bonds: A:D.104, A:Y.147, B:S.35 Salt bridges: A:K.159, B:K.40 L3P.12: 14 residues within 4Å: Chain A: Y.133, V.136, I.140 Chain B: R.7, W.10, A.14, T.17, A.18, F.54, L.61, L.62 Ligands: L3P.6, L3P.10, L3P.14 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.17, B:A.18, B:F.54, A:V.136, A:I.140 Salt bridges: B:R.7 Hydrogen bonds: A:Y.133 L3P.13: 9 residues within 4Å: Chain B: Y.131, F.135, A.139, V.187, L.190, G.197, I.198 Ligands: L3P.19, L3P.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.135, B:F.135, B:A.139, B:V.187, B:L.190, B:I.198, B:I.198 Hydrogen bonds: B:Y.131 L3P.14: 7 residues within 4Å: Chain A: A.143, L.146, Y.150, F.154 Ligands: L3P.6, L3P.10, L3P.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.143, A:L.146, A:Y.150 Hydrogen bonds: A:Y.150 L3P.17: 26 residues within 4Å: Chain B: D.104, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147, Y.150, K.159 Chain C: G.21, T.24, L.25, L.28, V.29, S.35, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.19, L3P.21 23 PLIP interactions: 13 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:A.110, B:A.114, B:I.117, B:I.117, B:A.143, B:A.144, B:Y.147, B:Y.147, B:Y.147, B:Y.150, C:L.25, C:L.28, C:V.29, C:T.47, C:L.48, C:L.48, C:A.51, C:F.54 Hydrogen bonds: B:D.104, B:Y.147, C:S.35 Salt bridges: B:K.159, C:K.40 L3P.19: 14 residues within 4Å: Chain B: Y.133, V.136, I.140 Chain C: R.7, W.10, A.14, T.17, A.18, F.54, L.61, L.62 Ligands: L3P.13, L3P.17, L3P.21 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:T.17, C:A.18, C:F.54, B:V.136, B:I.140 Salt bridges: C:R.7 Hydrogen bonds: B:Y.133 L3P.20: 9 residues within 4Å: Chain C: Y.131, F.135, A.139, V.187, L.190, G.197, I.198 Ligands: L3P.5, L3P.7 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.135, C:F.135, C:A.139, C:V.187, C:L.190, C:I.198, C:I.198 Hydrogen bonds: C:Y.131 L3P.21: 7 residues within 4Å: Chain B: A.143, L.146, Y.150, F.154 Ligands: L3P.13, L3P.17, L3P.19 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.143, B:L.146, B:Y.150 Hydrogen bonds: B:Y.150

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

L2P.4: 21 residues within 4Å: Chain A: L.87, L.109, G.113, G.116, G.120, T.121, L.127 Chain B: T.55, 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, L2P.11, L2P.18 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.80, B:W.80, B:W.80, B:A.84, B:F.88, B:F.88, B:F.88, B:L.92, B:L.123, B:L.127, A:L.87, A:L.87, A:L.109 Hydrogen bonds: B:Y.64 L2P.11: 21 residues within 4Å: Chain B: L.87, L.109, G.113, G.116, G.120, T.121, L.127 Chain C: T.55, M.56, Y.64, W.80, A.84, L.87, F.88, L.92, L.123, L.127 Ligands: L2P.4, GLC-MAN-GAL.8, GLC-MAN-GAL.8, L2P.18 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:L.87, B:L.87, B:L.109, C:W.80, C:W.80, C:W.80, C:A.84, C:F.88, C:F.88, C:F.88, C:L.92, C:L.123, C:L.127 Hydrogen bonds: C:Y.64 L2P.18: 21 residues within 4Å: Chain A: T.55, M.56, Y.64, W.80, A.84, L.87, F.88, L.92, L.123, L.127 Chain C: L.87, L.109, G.113, G.116, G.120, T.121, L.127 Ligands: L2P.4, L2P.11, GLC-MAN-GAL.15, GLC-MAN-GAL.15 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.80, A:W.80, A:W.80, A:A.84, A:F.88, A:F.88, A:F.88, A:L.92, A:L.123, A:L.127, C:L.87, C:L.87, C:L.109 Hydrogen bonds: A:Y.64

Links

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Citation

Matsui, Y. et al., Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin. J.MOL.BIOL. (2002)

Release Date

2002-12-18

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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