Structure of PDB 7ky8 Chain A Binding Site BS01

Receptor Information

>7ky8 Chain A (length=910) Species: 559292 (Saccharomyces cerevisiae S288C)

GFASVPLIVIVIITAIKDGIEDSRTKKSRISRELNFSVILNFVLLFILCF
TAGIVNGVYYKQKPRSRDYFEFGTIGGSASTNGFVSFWVAVILYQSLVPI
SLYISVEIIKTAQAIFIYTDVLLYNAKLDYPCTPKSWNISDDLGQIEYIF
SDKTGTLTQNVMEFKKCTINGVSYGRAYTEALAGLRKRQGVDVESEGRRE
KEEIAKDRETMIDELRSMSDNTQFCPEDLTFVSKEIVEDLKGSSGDHQQK
CCEHFLLALALCHSVLVEPNKDDPKKLDIKAQSPDESALVSTARQLGYSF
VGSSKSGLIVEIQGVQKEFQVLNVLEFNSSRKRMSCIIKIPGEPKALLIC
KGADSVIYSRLDRTQNDATLLEKTALHLEEYATEGLRTLCLAQRELTWSE
YERWVKTYDVAAASVTNREEELDKVTDVIERELILLGGTAIEDRLQDGVP
DSIALLAEAGIKLWVLTGDKVETAINIGFSCNVLNNDMELLVVKASGEDV
EEFGSDPIQVVNNLVTKYLREKFGMSGSEEELKEAKREHGLPQGNFAVII
DGDALKVALNGEEMRRKFLLLCKNCKAVLCCRVSPAQKAAVVKLVKKTLD
VMTLAIGDGSNDVAMIQSADVGVGIAGEEGRQAVMCSDYAIGQFRYVTRL
VLVHGKWCYKRLAEMIPQFFYKNVIFTLSLFWYGIYNNFDGSYLFEYTYL
TFYNLAFTSVPVILLAVLDQDVSDTVSMLVPQLYRVGILRKEWNQTKFLW
YMLDGVYQSVICFFFPYLAYHKNMVVTENGLGLDHRYFVGVFVTAIAVTS
CNFYVFMEQYRWDWFCGLFICLSLAVFYGWTGIWTSSSSSNEFYKGAARV
FAQPAYWAVLFVGVLFCLLPRFTIDCIRKIFYPKDIEIVREMWLRGDFDL
YPQGYDPTDP

Ligand information

• Ligand ID: CLR
• InChI: InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
• InChIKey: HVYWMOMLDIMFJA-DPAQBDIFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
  CACTVS 3.341: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
  ACDLabs 10.04: OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
  OpenEye OEToolkits 1.5.0: CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
  CACTVS 3.341: CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
• Formula: C27 H46 O
• Name: CHOLESTEROL
• ChEMBL: CHEMBL112570
• DrugBank: DB04540
• ZINC: ZINC000003875383
• PDB chain: 7ky8 Chain A Residue 1701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ky8 Transport mechanism of P4 ATPase phosphatidylcholine flippases.
• Resolution: 3.85 Å
• Binding residue (original residue number in PDB): L608 V615 F1246
• Binding residue (residue number reindexed from 1): L48 V55 F681
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 7.6.2.1: P-type phospholipid transporter.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0005215 transporter activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0015247 aminophospholipid flippase activity
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding
• GO:0090554 phosphatidylcholine floppase activity
• GO:0090555 phosphatidylethanolamine flippase activity
• GO:0090556 phosphatidylserine floppase activity
• GO:0140326 ATPase-coupled intramembrane lipid transporter activity
• GO:0140346 phosphatidylserine flippase activity
• GO:0140351 glycosylceramide flippase activity

Biological Process

• GO:0006869 lipid transport
• GO:0006897 endocytosis
• GO:0007163 establishment or maintenance of cell polarity
• GO:0015031 protein transport
• GO:0015914 phospholipid transport
• GO:0045332 phospholipid translocation
• GO:0099040 ceramide translocation
• GO:0140331 aminophospholipid translocation

Cellular Component

• GO:0005783 endoplasmic reticulum
• GO:0005886 plasma membrane
• GO:0005935 cellular bud neck
• GO:0016020 membrane
• GO:0070867 mating projection tip membrane
• GO:0071944 cell periphery
• GO:1990531 phospholipid-translocating ATPase complex

External links

• PDB: RCSB:7ky8, PDBe:7ky8, PDBj:7ky8
• PDBsum: 7ky8
• PubMed: 33320091
• UniProt: Q12675|ATC4_YEAST Phospholipid-transporting ATPase DNF2 (Gene Name=DNF2)