Structure of PDB 6jyd Chain A Binding Site BS01

Receptor Information

>6jyd Chain A (length=264) Species: 1454201 (Nonlabens marinus S1-08)

KNIESLFDYSAGQFEFIDHLLTMGVGVHFAALIFFLVVSQFVAPKYRIAT
ALSCIVMVSAGLILNSQAVMWTDAYAYVDGSYQLQDLTFSNGYRYVNWMA
TIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIITGYVGQLYEVDDIA
QLMIWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMMFAW
TLYPIAYLVPAFMNNADGVVLRQLLFTIADISSKVIYGLMITYIAIQQSA
AAGYVPAQQALGRI

Ligand information

• Ligand ID: RET
• InChI: InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+
• InChIKey: NCYCYZXNIZJOKI-OVSJKPMPSA-N
• SMILES:
  CACTVS 3.370: CC(=C\C=O)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C
  ACDLabs 12.01: O=C\C=C(\C=C\C=C(\C=C\C1=C(C)CCCC1(C)C)C)C
  OpenEye OEToolkits 1.7.0: CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C
  OpenEye OEToolkits 1.7.0: CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC=O)C)C
  CACTVS 3.370: CC(=CC=O)C=CC=C(C)C=CC1=C(C)CCCC1(C)C
• Formula: C20 H28 O
• Name: RETINAL
• ChEMBL: CHEMBL81379
• ZINC: ZINC000004228262
• PDB chain: 6jyd Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6jyd Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family.
• Resolution: 2.007 Å
• Binding residue (original residue number in PDB): W99 I103 L106 M135 S160 F164 W201 Y204 P205 Y208 K235
• Binding residue (residue number reindexed from 1): W98 I102 L105 M134 S159 F163 W200 Y203 P204 Y207 K234
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0009881 photoreceptor activity

Biological Process

• GO:0007602 phototransduction

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:6jyd, PDBe:6jyd, PDBj:6jyd
• PDBsum: 6jyd
• PubMed: 32083178
• UniProt: W8VZW3