SMTL ID : 4xxj.1

Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

33 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.1: 2 residues within 4Å: Chain A: W.81, L.124 Ligand excluded by PLIP LFA.2: 2 residues within 4Å: Chain A: Y.65, W.81 Ligand excluded by PLIP LFA.3: 7 residues within 4Å: Chain A: L.110, G.114, G.117, G.121 Chain C: I.53, T.56, M.57 Ligand excluded by PLIP LFA.4: 7 residues within 4Å: Chain A: I.53, T.56, M.57, F.89 Chain B: L.110, G.117, G.121 Ligand excluded by PLIP LFA.5: 2 residues within 4Å: Ligands: LFA.6, LFA.28 Ligand excluded by PLIP LFA.6: 5 residues within 4Å: Chain A: F.136, V.137, A.140 Ligands: LFA.5, LFA.7 Ligand excluded by PLIP LFA.7: 4 residues within 4Å: Chain A: Y.132, F.136, W.139 Ligands: LFA.6 Ligand excluded by PLIP LFA.8: 2 residues within 4Å: Chain A: I.5 Ligands: LFA.9 Ligand excluded by PLIP LFA.9: 3 residues within 4Å: Chain A: W.11, A.15 Ligands: LFA.8 Ligand excluded by PLIP LFA.10: 1 residues within 4Å: Chain A: I.199 Ligand excluded by PLIP LFA.11: 3 residues within 4Å: Chain A: N.177, V.181 Ligands: LFA.12 Ligand excluded by PLIP LFA.12: 4 residues within 4Å: Chain A: N.177, V.180, V.181 Ligands: LFA.11 Ligand excluded by PLIP LFA.13: 4 residues within 4Å: Chain A: L.20, G.24, V.214, G.219 Ligand excluded by PLIP LFA.15: 2 residues within 4Å: Chain B: W.81, L.88 Ligand excluded by PLIP LFA.16: 1 residues within 4Å: Ligands: LFA.24 Ligand excluded by PLIP LFA.17: 2 residues within 4Å: Chain B: F.136, A.140 Ligand excluded by PLIP LFA.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.19: 1 residues within 4Å: Ligands: LFA.29 Ligand excluded by PLIP LFA.20: 1 residues within 4Å: Chain B: A.15 Ligand excluded by PLIP LFA.21: 4 residues within 4Å: Chain B: L.20, G.24, V.214, V.218 Ligand excluded by PLIP LFA.22: 2 residues within 4Å: Chain B: N.177, V.181 Ligand excluded by PLIP LFA.24: 2 residues within 4Å: Chain C: Y.65 Ligands: LFA.16 Ligand excluded by PLIP LFA.25: 1 residues within 4Å: Chain C: W.81 Ligand excluded by PLIP LFA.26: 9 residues within 4Å: Chain B: T.56, M.57, F.89 Chain C: L.110, G.114, G.117, I.118, G.121, T.122 Ligand excluded by PLIP LFA.27: 1 residues within 4Å: Chain C: A.15 Ligand excluded by PLIP LFA.28: 3 residues within 4Å: Chain C: I.5, L.59 Ligands: LFA.5 Ligand excluded by PLIP LFA.29: 1 residues within 4Å: Ligands: LFA.19 Ligand excluded by PLIP LFA.30: 3 residues within 4Å: Chain C: S.133, F.136, V.137 Ligand excluded by PLIP LFA.31: 3 residues within 4Å: Chain C: Y.132, F.136, A.197 Ligand excluded by PLIP LFA.32: 1 residues within 4Å: Ligands: LFA.33 Ligand excluded by PLIP LFA.33: 2 residues within 4Å: Chain C: I.204 Ligands: LFA.32 Ligand excluded by PLIP LFA.34: 4 residues within 4Å: Chain C: L.20, Y.27, V.214, V.218 Ligand excluded by PLIP LFA.35: 3 residues within 4Å: Chain C: V.174, N.177, V.178 Ligand excluded by PLIP

3 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.14: 12 residues within 4Å: Chain A: T.108, A.111, A.145, Y.148 Chain C: G.22, L.29, K.41, Y.44, A.45, T.48, L.49, F.55 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.29, C:T.48, C:L.49, C:F.55, C:F.55, A:A.111, A:A.145 Hydrogen bonds: A:T.108 MPG.23: 17 residues within 4Å: Chain A: G.22, T.25, K.41, Y.44, A.45, T.48, L.49, A.52, F.55 Chain B: G.107, T.108, A.111, A.115, I.118, I.141, A.145, Y.148 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.111, B:A.115, B:I.118, B:I.141, B:A.145, B:Y.148, B:Y.148, A:T.25, A:T.48, A:L.49, A:A.52, A:F.55 Hydrogen bonds: B:T.108 Water bridges: A:T.48 MPG.36: 18 residues within 4Å: Chain B: G.22, L.26, L.29, K.41, Y.44, A.45, T.48, L.49, A.52, F.55 Chain C: G.107, T.108, A.111, A.115, I.118, I.141, A.145, Y.148 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.26, B:L.29, B:T.48, B:L.49, B:A.52, B:F.55, B:F.55, C:A.111, C:A.115, C:I.118, C:I.118, C:I.141, C:A.145, C:Y.148 Hydrogen bonds: B:K.41, C:T.108 Water bridges: B:T.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bratanov, D. et al., An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin. Plos One (2015)

Release Date

2015-07-01

Peptides

Bacteriorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin