Structure of PDB 6yby Chain A Binding Site BS02

Receptor Information

>6yby Chain A (length=270) Species: 308116 (Dokdonia eikasta)

TQELGANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKN
VDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGD
LFNNGYRYLNWLINVPMLLFQILFVVSLTTSKFSSVRNQFWFSGAMMIIT
GYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQK
ILSNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADV
SSKVIYGVLLGNLAITLSNK

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: 6yby Chain A Residue 336

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yby Molecular mechanism of light-driven sodium pumping.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): W113 V117 L120 M149 S174 S175 F178 W215 Y218 P219 Y222 S254 K255
• Binding residue (residue number reindexed from 1): W111 V115 L118 M147 S172 S173 F176 W213 Y216 P217 Y220 S252 K253
• Annotation score: 4

Gene Ontology

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:6yby, PDBe:6yby, PDBj:6yby
• PDBsum: 6yby
• PubMed: 32358514
• UniProt: N0DKS8