SMTL ID : 2zzl.1

Structure of bacteriorhodopsin's M intermediate at pH 7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 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: 9 residues within 4Å: Chain A: T.80, L.140, K.142 Chain B: Y.77, L.79, T.80, W.93 Ligands: L2P.4, SOG.8 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 Water bridges: A:K.142 GLC-MAN-SGA.9: 9 residues within 4Å: Chain B: T.80, L.140, K.142 Chain C: Y.77, L.79, T.80, W.93 Ligands: L2P.12, SOG.16 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 Water bridges: B:K.142 GLC-MAN-SGA.17: 9 residues within 4Å: Chain A: Y.77, L.79, T.80, W.93 Chain C: T.80, L.140, K.142 Ligands: L2P.20, SOG.24 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.80, A:L.79, A:T.80, A:W.93, C:K.142 Water bridges: C:K.142

3 x RET: RETINAL(Covalent)

RET.2: 18 residues within 4Å: Chain A: Y.96, W.99, T.102, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.96, A:T.103, A:M.158, A:W.195, 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:K.229 RET.10: 18 residues within 4Å: Chain B: Y.96, W.99, T.102, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.96, B:T.103, B:M.158, B:W.195, 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:K.229 RET.18: 18 residues within 4Å: Chain C: Y.96, W.99, T.102, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.96, C:T.103, C:M.158, C:W.195, 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:K.229

3 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.34, L.38, L.41, V.42, M.45, K.53, A.57, T.60, L.61, A.64, F.67 Chain C: D.117, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160, Y.163, F.167, G.168, S.171 Ligands: L1P.5, L1P.7 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:L.41, A:V.42, A:T.60, A:L.61, A:A.64, A:F.67, A:F.67, C:A.127, C:I.130, C:I.153, C:A.156, C:Y.160, C:Y.160, C:Y.163, C:Y.163 Hydrogen bonds: A:K.53, C:G.168, C:S.171 Salt bridges: A:K.53 L3P.11: 26 residues within 4Å: Chain A: D.117, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160, Y.163, F.167, G.168, S.171 Chain B: G.34, L.38, L.41, V.42, M.45, K.53, A.57, T.60, L.61, A.64, F.67 Ligands: L1P.13, L1P.15 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:L.41, B:V.42, B:T.60, B:L.61, B:A.64, B:F.67, B:F.67, A:A.127, A:I.130, A:I.153, A:A.156, A:Y.160, A:Y.160, A:Y.163, A:Y.163 Hydrogen bonds: B:K.53, A:G.168, A:S.171 Salt bridges: B:K.53 L3P.19: 26 residues within 4Å: Chain B: D.117, T.120, A.123, A.127, I.130, I.153, A.156, A.157, Y.160, Y.163, F.167, G.168, S.171 Chain C: G.34, L.38, L.41, V.42, M.45, K.53, A.57, T.60, L.61, A.64, F.67 Ligands: L1P.21, L1P.23 19 PLIP interactions: 9 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:L.41, C:V.42, C:T.60, C:L.61, C:A.64, C:F.67, C:F.67, B:A.127, B:I.130, B:I.153, B:A.156, B:Y.160, B:Y.160, B:Y.163, B:Y.163 Hydrogen bonds: C:K.53, B:G.168, B:S.171 Salt bridges: C:K.53

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

L2P.4: 16 residues within 4Å: Chain A: L.100, L.122, G.129, I.130, G.133, L.140 Chain B: I.65, T.68, Y.77, W.93, A.97, L.100, F.101, L.136, L.140 Ligands: GLC-MAN-SGA.1 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.65, B:W.93, B:W.93, B:W.93, B:W.93, B:L.100, B:F.101, B:F.101, B:F.101, B:F.101, B:L.136, B:L.140, A:L.100, A:L.122 Hydrogen bonds: B:Y.77 L2P.12: 16 residues within 4Å: Chain B: L.100, L.122, G.129, I.130, G.133, L.140 Chain C: I.65, T.68, Y.77, W.93, A.97, L.100, F.101, L.136, L.140 Ligands: GLC-MAN-SGA.9 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain C Hydrophobic interactions: B:L.100, B:L.122, C:I.65, C:W.93, C:W.93, C:W.93, C:W.93, C:L.100, C:F.101, C:F.101, C:F.101, C:F.101, C:L.136, C:L.140 Hydrogen bonds: C:Y.77 L2P.20: 16 residues within 4Å: Chain A: I.65, T.68, Y.77, W.93, A.97, L.100, F.101, L.136, L.140 Chain C: L.100, L.122, G.129, I.130, G.133, L.140 Ligands: GLC-MAN-SGA.17 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.65, A:W.93, A:W.93, A:W.93, A:W.93, A:L.100, A:F.101, A:F.101, A:F.101, A:F.101, A:L.136, A:L.140, C:L.100, C:L.122 Hydrogen bonds: A:Y.77

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

L1P.5: 13 residues within 4Å: Chain A: R.20, W.23, A.27, T.30, A.31, F.67, L.74, L.75 Chain C: Y.146, V.149, I.153 Ligands: L3P.3, L1P.22 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:V.149, C:I.153, A:W.23, A:T.30, A:A.31, A:F.67 Hydrogen bonds: C:Y.146, C:Y.146 Salt bridges: A:R.20 L1P.6: 8 residues within 4Å: Chain A: Y.144, F.148, W.151, A.152, L.203, A.209, I.211 Ligands: L1P.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.148, A:F.148, A:W.151, A:A.152, A:L.203, A:L.203, A:A.209, A:I.211 Hydrogen bonds: A:Y.144 L1P.7: 5 residues within 4Å: Chain C: A.156, L.159, Y.163, F.167 Ligands: L3P.3 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.156, C:L.159, C:Y.163 L1P.13: 13 residues within 4Å: Chain A: Y.146, V.149, I.153 Chain B: R.20, W.23, A.27, T.30, A.31, F.67, L.74, L.75 Ligands: L1P.6, L3P.11 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.23, B:T.30, B:A.31, B:F.67, A:V.149, A:I.153 Salt bridges: B:R.20 Hydrogen bonds: A:Y.146, A:Y.146 L1P.14: 8 residues within 4Å: Chain B: Y.144, F.148, W.151, A.152, L.203, A.209, I.211 Ligands: L1P.21 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.148, B:F.148, B:W.151, B:A.152, B:L.203, B:L.203, B:A.209, B:I.211 Hydrogen bonds: B:Y.144 L1P.15: 5 residues within 4Å: Chain A: A.156, L.159, Y.163, F.167 Ligands: L3P.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.156, A:L.159, A:Y.163 L1P.21: 13 residues within 4Å: Chain B: Y.146, V.149, I.153 Chain C: R.20, W.23, A.27, T.30, A.31, F.67, L.74, L.75 Ligands: L1P.14, L3P.19 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.23, C:T.30, C:A.31, C:F.67, B:V.149, B:I.153 Salt bridges: C:R.20 Hydrogen bonds: B:Y.146, B:Y.146 L1P.22: 8 residues within 4Å: Chain C: Y.144, F.148, W.151, A.152, L.203, A.209, I.211 Ligands: L1P.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.148, C:F.148, C:W.151, C:A.152, C:L.203, C:L.203, C:A.209, C:I.211 Hydrogen bonds: C:Y.144 L1P.23: 5 residues within 4Å: Chain B: A.156, L.159, Y.163, F.167 Ligands: L3P.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.156, B:L.159, B:Y.163

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

SOG.8: 10 residues within 4Å: Chain A: L.140, T.141, K.142, V.143, Y.146 Chain B: L.75, G.76, Y.77 Ligands: GLC-MAN-SGA.1, GLC-MAN-SGA.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.75, B:Y.77, A:K.142, A:K.142 Water bridges: A:T.141 SOG.16: 10 residues within 4Å: Chain B: L.140, T.141, K.142, V.143, Y.146 Chain C: L.75, G.76, Y.77 Ligands: GLC-MAN-SGA.9, GLC-MAN-SGA.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.142, B:K.142, C:L.75, C:Y.77 Water bridges: B:T.141 SOG.24: 10 residues within 4Å: Chain A: L.75, G.76, Y.77 Chain C: L.140, T.141, K.142, V.143, Y.146 Ligands: GLC-MAN-SGA.17, GLC-MAN-SGA.17 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.142, C:K.142, A:L.75, A:Y.77 Water bridges: C:T.141

Links

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Citation

Yamamoto, M. et al., Crystal Structures of Different Substates of Bacteriorhodopsin's M Intermediate at Various pH Levels. J.Mol.Biol. (2009)

Release Date

2009-10-06

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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