SMTL ID : 1ucq.1

Crystal structure of the L intermediate of bacteriorhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 16 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.83, A:T.89, A:T.90, A:L.93, A:M.145, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:K.216 RET.9: 16 residues within 4Å: Chain B: Y.83, W.86, T.89, T.90, L.93, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.83, B:T.89, B:T.90, B:L.93, 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: 16 residues within 4Å: Chain C: Y.83, W.86, T.89, T.90, L.93, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.83, C:T.89, C:T.90, C:L.93, C:M.145, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, 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: 27 residues within 4Å: Chain A: G.21, T.24, L.25, L.28, V.29, M.32, S.35, P.37, 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, Y.147, Y.150, K.159 Ligands: L3P.5, L3P.7 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:T.24, A:L.25, A:L.28, A:V.29, A:T.47, A:L.48, A:F.54, A:F.54, C:I.117, C:A.143, C:Y.147, C:Y.147, C:Y.150, C:Y.150 Hydrogen bonds: A:S.35, C:D.104 Water bridges: A:T.47, C:K.159 Salt bridges: A:K.40, A:K.40, C:K.159 L3P.5: 12 residues within 4Å: Chain A: R.7, W.10, A.14, F.54, L.61, L.62 Chain C: Y.133, V.136, I.140 Ligands: L3P.3, L3P.7, L3P.20 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.54, A:L.61, C:V.136, C:I.140 Salt bridges: A:R.7 L3P.6: 8 residues within 4Å: Chain A: Y.131, F.135, A.139, L.190, A.196, I.198 Ligands: L3P.12, L3P.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.135, A:A.139, A:L.190, A:A.196, 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 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.143, C:L.146, C:L.146, C:Y.150 Hydrogen bonds: C:Y.150 L3P.10: 27 residues within 4Å: Chain A: D.104, T.107, A.110, A.114, I.117, I.140, A.143, Y.147, Y.150, K.159 Chain B: G.21, T.24, L.25, L.28, V.29, M.32, S.35, P.37, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.12, L3P.14 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:I.117, A:A.143, A:Y.147, A:Y.147, A:Y.150, A:Y.150, B:T.24, B:L.25, B:L.28, B:V.29, B:T.47, B:L.48, B:F.54, B:F.54 Hydrogen bonds: A:D.104, B:S.35 Water bridges: A:K.159, B:T.47 Salt bridges: A:K.159, B:K.40, B:K.40 L3P.12: 12 residues within 4Å: Chain A: Y.133, V.136, I.140 Chain B: R.7, W.10, A.14, F.54, L.61, L.62 Ligands: L3P.6, L3P.10, L3P.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.54, B:L.61, A:V.136, A:I.140 Salt bridges: B:R.7 L3P.13: 8 residues within 4Å: Chain B: Y.131, F.135, A.139, L.190, A.196, I.198 Ligands: L3P.19, L3P.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.135, B:A.139, B:L.190, B:A.196, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.143, A:L.146, A:L.146, A:Y.150 Hydrogen bonds: A:Y.150 L3P.17: 27 residues within 4Å: Chain B: D.104, T.107, A.110, A.114, I.117, I.140, A.143, Y.147, Y.150, K.159 Chain C: G.21, T.24, L.25, L.28, V.29, M.32, S.35, P.37, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: L3P.19, L3P.21 21 PLIP interactions: 9 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:I.117, B:A.143, B:Y.147, B:Y.147, B:Y.150, B:Y.150, C:T.24, C:L.25, C:L.28, C:V.29, C:T.47, C:L.48, C:F.54, C:F.54 Hydrogen bonds: B:D.104, C:S.35 Water bridges: B:K.159, C:T.47 Salt bridges: B:K.159, C:K.40, C:K.40 L3P.19: 12 residues within 4Å: Chain B: Y.133, V.136, I.140 Chain C: R.7, W.10, A.14, F.54, L.61, L.62 Ligands: L3P.13, L3P.17, L3P.21 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.54, C:L.61, B:V.136, B:I.140 Salt bridges: C:R.7 L3P.20: 8 residues within 4Å: Chain C: Y.131, F.135, A.139, L.190, A.196, I.198 Ligands: L3P.5, L3P.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.135, C:A.139, C:L.190, C:A.196, 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.143, B:L.146, B:L.146, B:Y.150 Hydrogen bonds: B:Y.150

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

L2P.4: 18 residues within 4Å: Chain A: L.87, L.109, G.113, G.116, G.120, T.121 Chain B: M.56, Y.64, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: GLC-MAN-GAL.1, GLC-MAN-GAL.1, L2P.11, L2P.18 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:L.87, A:L.87, A:L.109, 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:F.88, B:L.127 L2P.11: 18 residues within 4Å: Chain B: L.87, L.109, G.113, G.116, G.120, T.121 Chain C: M.56, Y.64, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: L2P.4, GLC-MAN-GAL.8, GLC-MAN-GAL.8, L2P.18 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: 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:F.88, C:L.127, B:L.87, B:L.87, B:L.109 L2P.18: 18 residues within 4Å: Chain A: M.56, Y.64, W.80, A.84, L.87, F.88, L.123, L.127 Chain C: L.87, L.109, G.113, G.116, G.120, T.121 Ligands: L2P.4, L2P.11, GLC-MAN-GAL.15, GLC-MAN-GAL.15 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain A Hydrophobic interactions: C:L.87, C:L.87, C:L.109, 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:F.88, A:L.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kouyama, T. et al., Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle. J.Mol.Biol. (2004)

Release Date

2003-12-30

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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