SMTL ID : 2zfe.1

Crystal structure of bacteriorhodopsin-xenon complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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

GLC-MAN-SGA.1: 9 residues within 4Å: Chain A: T.80, P.83, L.140, K.142 Chain B: Y.77, L.79, T.80, W.93 Ligands: L2P.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.80, B:T.80, B:T.80, B:W.93, A:K.142 Water bridges: A:T.80, B:M.81 GLC-MAN-SGA.9: 9 residues within 4Å: Chain B: T.80, P.83, L.140, K.142 Chain C: Y.77, L.79, T.80, W.93 Ligands: L2P.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.80, C:T.80, C:T.80, C:W.93, B:K.142 Water bridges: B:T.80, C:M.81 GLC-MAN-SGA.17: 9 residues within 4Å: Chain A: Y.77, L.79, T.80, W.93 Chain C: T.80, P.83, L.140, K.142 Ligands: L2P.20 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:T.80, C:K.142, A:T.80, A:T.80, A:W.93 Water bridges: C:T.80, A:M.81

3 x RET: RETINAL(Covalent)

RET.2: 17 residues within 4Å: Chain A: Y.96, W.99, T.102, T.103, L.106, 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:T.102, A:T.103, A:L.106, 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.10: 17 residues within 4Å: Chain B: Y.96, W.99, T.102, T.103, L.106, 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:T.102, B:T.103, B:L.106, 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.18: 17 residues within 4Å: Chain C: Y.96, W.99, T.102, T.103, L.106, 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:T.102, C:T.103, C:L.106, 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 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, T.37, L.38, L.41, V.42, M.45, S.48, K.53, Y.56, 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 Ligands: L1P.5, L1P.7 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:T.37, A:L.38, A:L.41, A:L.41, A:V.42, A:T.60, A:L.61, A:L.61, A:F.67, A:F.67, C:I.130, C:I.153, C:A.156, C:Y.160, C:Y.160, C:Y.163, C:Y.163 Hydrogen bonds: A:S.48, C:D.117 Water bridges: A:T.60 Salt bridges: A:K.53, C:K.172 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 Chain B: G.34, T.37, L.38, L.41, V.42, M.45, S.48, K.53, Y.56, A.57, T.60, L.61, A.64, F.67 Ligands: L1P.13, L1P.15 22 PLIP interactions: 9 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:I.130, A:I.153, A:A.156, A:Y.160, A:Y.160, A:Y.163, A:Y.163, B:T.37, B:L.38, B:L.41, B:L.41, B:V.42, B:T.60, B:L.61, B:L.61, B:F.67, B:F.67 Hydrogen bonds: A:D.117, B:S.48 Salt bridges: A:K.172, B:K.53 Water bridges: B:T.60 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 Chain C: G.34, T.37, L.38, L.41, V.42, M.45, S.48, K.53, Y.56, A.57, T.60, L.61, A.64, F.67 Ligands: L1P.21, L1P.23 22 PLIP interactions: 9 interactions with chain B, 13 interactions with chain C Hydrophobic interactions: B:I.130, B:I.153, B:A.156, B:Y.160, B:Y.160, B:Y.163, B:Y.163, C:T.37, C:L.38, C:L.41, C:L.41, C:V.42, C:T.60, C:L.61, C:L.61, C:F.67, C:F.67 Hydrogen bonds: B:D.117, C:S.48 Salt bridges: B:K.172, C:K.53 Water bridges: C:T.60

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

L2P.4: 23 residues within 4Å: Chain A: L.100, F.101, L.122, V.125, G.126, G.129, I.130, G.133, L.140 Chain B: I.65, M.69, Y.77, W.93, Y.96, A.97, L.100, F.101, L.136, L.140 Ligands: GLC-MAN-SGA.1, GLC-MAN-SGA.1, L2P.12, L2P.20 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.93, B:W.93, B:L.100, B:F.101, B:F.101, B:F.101, B:F.101, B:F.101, B:L.136, B:L.140, A:L.100, A:L.100, A:L.100, A:F.101, A:L.122, A:V.125 Hydrogen bonds: B:Y.77 L2P.12: 23 residues within 4Å: Chain B: L.100, F.101, L.122, V.125, G.126, G.129, I.130, G.133, L.140 Chain C: I.65, M.69, Y.77, W.93, Y.96, A.97, L.100, F.101, L.136, L.140 Ligands: L2P.4, GLC-MAN-SGA.9, GLC-MAN-SGA.9, L2P.20 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.93, C:W.93, C:L.100, C:F.101, C:F.101, C:F.101, C:F.101, C:F.101, C:L.136, C:L.140, B:L.100, B:L.100, B:L.100, B:F.101, B:L.122, B:V.125 Hydrogen bonds: C:Y.77 L2P.20: 23 residues within 4Å: Chain A: I.65, M.69, Y.77, W.93, Y.96, A.97, L.100, F.101, L.136, L.140 Chain C: L.100, F.101, L.122, V.125, G.126, G.129, I.130, G.133, L.140 Ligands: L2P.4, L2P.12, GLC-MAN-SGA.17, GLC-MAN-SGA.17 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:W.93, A:W.93, A:L.100, A:F.101, A:F.101, A:F.101, A:F.101, A:F.101, A:L.136, A:L.140, C:L.100, C:L.100, C:L.100, C:F.101, C:L.122, C:V.125 Hydrogen bonds: A:Y.77

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

L1P.5: 11 residues within 4Å: Chain A: R.20, A.27, T.30, F.67, L.74, L.75 Chain C: Y.146, V.149, I.153 Ligands: L3P.3, L1P.7 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.30, A:F.67, A:L.74, C:V.149, C:I.153 Salt bridges: A:R.20 L1P.6: 6 residues within 4Å: Chain A: Y.144, F.148, A.152, V.200, A.209, I.211 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.148, A:F.148, A:F.148, A:A.152, A:V.200, A:A.209, A:I.211 Hydrogen bonds: A:Y.144 L1P.7: 6 residues within 4Å: Chain C: A.156, L.159, Y.163, F.167 Ligands: L3P.3, L1P.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.156, C:L.159, C:Y.163 Hydrogen bonds: C:Y.163 L1P.13: 11 residues within 4Å: Chain A: Y.146, V.149, I.153 Chain B: R.20, A.27, T.30, F.67, L.74, L.75 Ligands: L3P.11, L1P.15 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.149, A:I.153, B:T.30, B:F.67, B:L.74 Salt bridges: B:R.20 L1P.14: 6 residues within 4Å: Chain B: Y.144, F.148, A.152, V.200, A.209, I.211 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.148, B:F.148, B:F.148, B:A.152, B:V.200, B:A.209, B:I.211 Hydrogen bonds: B:Y.144 L1P.15: 6 residues within 4Å: Chain A: A.156, L.159, Y.163, F.167 Ligands: L3P.11, L1P.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.156, A:L.159, A:Y.163 Hydrogen bonds: A:Y.163 L1P.21: 11 residues within 4Å: Chain B: Y.146, V.149, I.153 Chain C: R.20, A.27, T.30, F.67, L.74, L.75 Ligands: L3P.19, L1P.23 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:V.149, B:I.153, C:T.30, C:F.67, C:L.74 Salt bridges: C:R.20 L1P.22: 6 residues within 4Å: Chain C: Y.144, F.148, A.152, V.200, A.209, I.211 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.148, C:F.148, C:F.148, C:A.152, C:V.200, C:A.209, C:I.211 Hydrogen bonds: C:Y.144 L1P.23: 6 residues within 4Å: Chain B: A.156, L.159, Y.163, F.167 Ligands: L3P.19, L1P.21 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.156, B:L.159, B:Y.163 Hydrogen bonds: B:Y.163

3 x XE: XENON(Non-covalent)

XE.8: 4 residues within 4Å: Chain A: L.107, L.108, I.121, V.125 No protein-ligand interaction detected (PLIP) XE.16: 4 residues within 4Å: Chain B: L.107, L.108, I.121, V.125 No protein-ligand interaction detected (PLIP) XE.24: 4 residues within 4Å: Chain C: L.107, L.108, I.121, V.125 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayakawa, N. et al., Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin. J.Mol.Biol. (2008)

Release Date

2008-11-11

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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