SMTL ID : 3vhz.1

Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

GLC-MAN-SGA.1: 10 residues within 4Å: Chain A: T.80, M.81, L.140, K.142 Chain B: Y.77, L.79, T.80, W.93 Ligands: L2P.4, L2P.12 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.80, B:L.79, B:T.80, B:W.93, A:K.142 GLC-MAN-SGA.5: 10 residues within 4Å: Chain B: T.80, M.81, L.140, K.142 Chain C: Y.77, L.79, T.80, W.93 Ligands: L2P.4, L2P.8 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.80, B:K.142, C:L.79, C:T.80, C:W.93 GLC-MAN-SGA.9: 10 residues within 4Å: Chain A: Y.77, L.79, T.80, W.93 Chain C: T.80, M.81, L.140, K.142 Ligands: L2P.8, L2P.12 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.80, C:K.142, A:L.79, A:T.80, A:W.93

3 x RET: RETINAL(Covalent)

RET.2: 16 residues within 4Å: Chain A: Y.96, W.99, T.102, T.103, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.96, A:W.99, A:T.102, A:T.103, A:M.158, A:W.195, A:Y.198, A:Y.198, A:Y.198, A:Y.198, A:P.199, A:W.202, A:W.202, A:A.228, A:K.229 RET.6: 16 residues within 4Å: Chain B: Y.96, W.99, T.102, T.103, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.96, B:W.99, B:T.102, B:T.103, B:M.158, B:W.195, B:Y.198, B:Y.198, B:Y.198, B:Y.198, B:P.199, B:W.202, B:W.202, B:A.228, B:K.229 RET.10: 16 residues within 4Å: Chain C: Y.96, W.99, T.102, T.103, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.96, C:W.99, C:T.102, C:T.103, C:M.158, C:W.195, C:Y.198, C:Y.198, C:Y.198, C:Y.198, C:P.199, C:W.202, C:W.202, C:A.228, C:K.229

3 x SOG: octyl 1-thio-beta-D-glucopyranoside(Non-covalent)

SOG.3: 13 residues within 4Å: Chain A: L.41, G.44, V.47, K.53, Y.56, A.57, T.60, L.61 Chain C: T.120, A.123, A.157, Y.160, V.164 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.60, A:L.61, C:A.157 Hydrogen bonds: A:G.44, A:K.53, C:Y.160 Water bridges: A:Y.56 SOG.7: 13 residues within 4Å: Chain A: T.120, A.123, A.157, Y.160, V.164 Chain B: L.41, G.44, V.47, K.53, Y.56, A.57, T.60, L.61 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.60, B:L.61, A:A.157 Hydrogen bonds: B:G.44, B:K.53, A:Y.160 Water bridges: B:Y.56 SOG.11: 13 residues within 4Å: Chain B: T.120, A.123, A.157, Y.160, V.164 Chain C: L.41, G.44, V.47, K.53, Y.56, A.57, T.60, L.61 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:T.60, C:L.61, B:A.157 Hydrogen bonds: C:G.44, C:K.53, B:Y.160 Water bridges: C:Y.56

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

L2P.4: 22 residues within 4Å: Chain A: L.100, L.122, G.129, G.133, T.134, L.136 Chain B: L.61, T.68, M.69, Y.77, W.93, Y.96, A.97, F.101, L.105, L.136, L.140 Ligands: GLC-MAN-SGA.1, GLC-MAN-SGA.1, GLC-MAN-SGA.5, L2P.8, L2P.12 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.100, A:L.100, A:L.122, A:L.136, B:L.61, B:W.93, B:W.93, B:Y.96, B:F.101, B:F.101, B:L.105, B:L.136, B:L.140 Hydrogen bonds: B:Y.77 L2P.8: 22 residues within 4Å: Chain B: L.100, L.122, G.129, G.133, T.134, L.136 Chain C: L.61, T.68, M.69, Y.77, W.93, Y.96, A.97, F.101, L.105, L.136, L.140 Ligands: L2P.4, GLC-MAN-SGA.5, GLC-MAN-SGA.5, GLC-MAN-SGA.9, L2P.12 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.61, C:W.93, C:W.93, C:Y.96, C:F.101, C:F.101, C:L.105, C:L.136, C:L.140, B:L.100, B:L.100, B:L.122, B:L.136 Hydrogen bonds: C:Y.77 L2P.12: 22 residues within 4Å: Chain A: L.61, T.68, M.69, Y.77, W.93, Y.96, A.97, F.101, L.105, L.136, L.140 Chain C: L.100, L.122, G.129, G.133, T.134, L.136 Ligands: GLC-MAN-SGA.1, L2P.4, L2P.8, GLC-MAN-SGA.9, GLC-MAN-SGA.9 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.61, A:W.93, A:W.93, A:Y.96, A:F.101, A:F.101, A:L.105, A:L.136, A:L.140, C:L.100, C:L.100, C:L.122, C:L.136 Hydrogen bonds: A:Y.77

Links

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Citation

Zhang, J. et al., Crystal structure of the O intermediate of the Leu93Ala mutant of bacteriorhodopsin. Proteins (2012)

Release Date

2012-06-13

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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