SMTL ID : 5b35.1

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 18 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.83, A:T.90, A:L.93, A:M.145, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:A.215, A:K.216

1 x 4QM: (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol(Non-covalent)

4QM.2: 4 residues within 4Å: Chain A: R.7, W.10, L.61, L.62 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.10 Hydrogen bonds: A:R.7

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

OCT.3: 3 residues within 4Å: Chain A: S.214 Ligands: D10.4, D10.7 No protein-ligand interaction detected (PLIP)

5 x D10: DECANE(Non-covalent)

D10.4: 5 residues within 4Å: Chain A: G.218, I.222, R.225 Ligands: OCT.3, D10.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.222 D10.6: 1 residues within 4Å: Chain A: V.199 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.199 D10.7: 4 residues within 4Å: Chain A: N.176, V.180 Ligands: OCT.3, D10.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.180 D10.8: 3 residues within 4Å: Chain A: A.143, Y.150 Ligands: R16.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.150 D10.10: 2 residues within 4Å: Chain A: F.54 Ligands: D12.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.54

3 x D12: DODECANE(Non-covalent)

D12.5: 1 residues within 4Å: Chain A: I.203 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.203 D12.14: 3 residues within 4Å: Chain A: I.140, Y.147 Ligands: DD9.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.140 D12.15: 4 residues within 4Å: Chain A: A.44, T.47, L.48 Ligands: D10.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.44, A:T.47, A:L.48

2 x R16: HEXADECANE(Non-covalent)

R16.9: 5 residues within 4Å: Chain A: L.149, Y.150, F.153, V.179 Ligands: D10.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.153, A:V.179 R16.17: 4 residues within 4Å: Chain A: W.10, I.11, A.14, L.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.10, A:W.10, A:I.11, A:L.15

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

HP6.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.12: 1 residues within 4Å: Chain A: K.30 No protein-ligand interaction detected (PLIP)

2 x DD9: nonane(Non-covalent)

DD9.13: 2 residues within 4Å: Chain A: Y.133, W.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.133, A:W.137, A:W.137 DD9.16: 3 residues within 4Å: Chain A: G.106, L.109 Ligands: D12.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.109

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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