SMTL ID : 4x32.1

Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.82, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.82, A:T.86, A:L.89, A:M.141, A:W.178, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:W.185, A:A.211, A:K.212 RET.10: 16 residues within 4Å: Chain B: W.82, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.82, B:T.86, B:L.89, B:M.141, B:W.178, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:P.182, B:W.185, B:A.211, B:K.212 RET.19: 16 residues within 4Å: Chain C: W.82, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.82, C:T.86, C:L.89, C:M.141, C:W.178, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:P.182, C:W.185, C:A.211, C:K.212

24 x LI1: 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL(Non-covalent)

LI1.2: 5 residues within 4Å: Chain A: W.76, L.83, L.119, L.123 Ligands: LI1.7 Ligand excluded by PLIP LI1.3: 4 residues within 4Å: Chain A: S.128, F.131, V.132, A.135 Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Chain A: V.132, I.136 Chain C: L.54 Ligand excluded by PLIP LI1.5: 4 residues within 4Å: Chain A: A.10, T.13, A.14, L.57 Ligand excluded by PLIP LI1.6: 20 residues within 4Å: Chain A: G.17, T.20, L.21, L.24, G.27, V.30, K.36, Y.39, A.40, T.43, L.44, F.50 Chain B: G.102, T.103, A.106, A.110, I.113, I.136, A.140, Y.143 Ligand excluded by PLIP LI1.7: 15 residues within 4Å: Chain A: I.48, T.51, M.52, Y.60, W.76, F.84 Chain B: V.108, G.109, G.112, I.113, G.116, T.117, V.120, L.123 Ligands: LI1.2 Ligand excluded by PLIP LI1.8: 4 residues within 4Å: Chain A: Y.127, F.131, W.134 Ligands: LI1.9 Ligand excluded by PLIP LI1.9: 2 residues within 4Å: Chain A: L.186 Ligands: LI1.8 Ligand excluded by PLIP LI1.11: 5 residues within 4Å: Chain B: W.76, L.83, L.119, L.123 Ligands: LI1.16 Ligand excluded by PLIP LI1.12: 4 residues within 4Å: Chain B: S.128, F.131, V.132, A.135 Ligand excluded by PLIP LI1.13: 3 residues within 4Å: Chain A: L.54 Chain B: V.132, I.136 Ligand excluded by PLIP LI1.14: 4 residues within 4Å: Chain B: A.10, T.13, A.14, L.57 Ligand excluded by PLIP LI1.15: 20 residues within 4Å: Chain B: G.17, T.20, L.21, L.24, G.27, V.30, K.36, Y.39, A.40, T.43, L.44, F.50 Chain C: G.102, T.103, A.106, A.110, I.113, I.136, A.140, Y.143 Ligand excluded by PLIP LI1.16: 15 residues within 4Å: Chain B: I.48, T.51, M.52, Y.60, W.76, F.84 Chain C: V.108, G.109, G.112, I.113, G.116, T.117, V.120, L.123 Ligands: LI1.11 Ligand excluded by PLIP LI1.17: 4 residues within 4Å: Chain B: Y.127, F.131, W.134 Ligands: LI1.18 Ligand excluded by PLIP LI1.18: 2 residues within 4Å: Chain B: L.186 Ligands: LI1.17 Ligand excluded by PLIP LI1.20: 5 residues within 4Å: Chain C: W.76, L.83, L.119, L.123 Ligands: LI1.25 Ligand excluded by PLIP LI1.21: 4 residues within 4Å: Chain C: S.128, F.131, V.132, A.135 Ligand excluded by PLIP LI1.22: 3 residues within 4Å: Chain B: L.54 Chain C: V.132, I.136 Ligand excluded by PLIP LI1.23: 4 residues within 4Å: Chain C: A.10, T.13, A.14, L.57 Ligand excluded by PLIP LI1.24: 20 residues within 4Å: Chain A: G.102, T.103, A.106, A.110, I.113, I.136, A.140, Y.143 Chain C: G.17, T.20, L.21, L.24, G.27, V.30, K.36, Y.39, A.40, T.43, L.44, F.50 Ligand excluded by PLIP LI1.25: 15 residues within 4Å: Chain A: V.108, G.109, G.112, I.113, G.116, T.117, V.120, L.123 Chain C: I.48, T.51, M.52, Y.60, W.76, F.84 Ligands: LI1.20 Ligand excluded by PLIP LI1.26: 4 residues within 4Å: Chain C: Y.127, F.131, W.134 Ligands: LI1.27 Ligand excluded by PLIP LI1.27: 2 residues within 4Å: Chain C: L.186 Ligands: LI1.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogly, P. et al., Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. Iucrj (2015)

Release Date

2015-02-18

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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