SMTL ID : 5b34.1

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.83, A:T.90, A:L.93, A:M.145, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:P.186, A:W.189, A:A.215, A:K.216

2 x 4QL: 2,4,6-tris(iodanyl)-5-(octanoylamino)benzene-1,3-dicarboxylic acid(Non-covalent)

4QL.2: 5 residues within 4Å: Chain A: V.173, N.176, V.180 Ligands: OCT.4, HP6.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.173, A:N.176, A:V.180 Hydrogen bonds: A:N.176 Water bridges: A:S.169 4QL.3: 7 residues within 4Å: Chain A: E.166, T.170, I.222, S.226, R.227 Ligands: OCT.5, HP6.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.227 Halogen bonds: A:I.222

2 x OCT: N-OCTANE(Non-covalent)

OCT.4: 4 residues within 4Å: Chain A: V.173, N.176, V.177 Ligands: 4QL.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.176, A:V.177 OCT.5: 3 residues within 4Å: Chain A: L.221, R.225 Ligands: 4QL.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.221, A:L.221

4 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.6: 5 residues within 4Å: Chain A: A.143, Y.147, Y.150, V.151, G.155 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.150, A:V.151 D12.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.16: 3 residues within 4Å: Chain A: A.110, A.144, Y.147 No protein-ligand interaction detected (PLIP) D12.17: 5 residues within 4Å: Chain A: G.31, Y.43, A.44, T.47 Ligands: D10.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.43

3 x D10: DECANE(Non-covalent)

D10.7: 2 residues within 4Å: Chain A: W.10, A.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.10, A:A.14 D10.8: 2 residues within 4Å: Chain A: L.211, S.214 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.211 D10.10: 2 residues within 4Å: Chain A: T.55 Ligands: D12.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.55

1 x R16: HEXADECANE(Non-covalent)

R16.9: 4 residues within 4Å: Chain A: L.146, L.149, Y.150, V.179 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.146, A:Y.150, A:V.179

3 x HP6: HEPTANE(Non-functional Binders)(Non-covalent)

HP6.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.12: 2 residues within 4Å: Ligands: 4QL.2, 4QL.3 No protein-ligand interaction detected (PLIP) HP6.13: 2 residues within 4Å: Chain A: Y.26, K.30 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.26

2 x DD9: nonane(Non-covalent)

DD9.14: 2 residues within 4Å: Chain A: Y.133, W.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.133, A:W.137 DD9.18: 1 residues within 4Å: Chain A: V.217 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakane, T. et al., Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-11-09

Peptides

Bacteriorhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin

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