Structure of PDB 8edw Chain A Binding Site BS01

Receptor Information
>8edw Chain A (length=1804) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FWTQLMLLLWKNFMYRRRQPVQLLVELLWPLFLFFILVAVRHSHPPLEHH
ECHFPNKPLPSAGTVPWLQGLICNVNNTCFPQLTPGEEPGRLSNFNDSLV
SRLLADARTVLGGASAHRAEDLAQELLALRSLVELRALLQRPRGTSGPLE
LLSEALCSPACSELIGALDSHPLSRLLWRRLKPLILGKLLFAPDTPFTRK
LMAQVNRTFEELTLLRDVREVWEMLGPRIFTFMDAHADVGHLVGTLGRVT
ECLSLDKLEAAPSEAALVSRALQLLAEHRFWAGVVFLGPEDSSDPTEHPT
PDLGPGHVRIKIRMDIDVVTRTNKIRDRFWDPGPAADPLTDLRYVWGGFV
YLQDLVERAAVRVLSGANPRAGLYLQQMPYPCYVDDVFLRVLSRSLPLFL
TLAWIYSVTLTVKAVVREKETRLRDTMRAMGLSRAVLWLGWFLSCLGPFL
LSAALLVLVLKLGDILPYSHPGVVFLFLAAFAVATVTQSFLLSAFFSRAN
LAAACGGLAYFSLYLPYVLCVAWRDRLPAGGRVAASLLSPVAFGFGCESL
ALLEEQGEGAQWHNVGTRPTADVFSLAQVSGLLLLDAALYGLATWYLEAV
CPGQYGVLVEEAPPGLSPGVSVRSLEKRFPGSPQPALRGLSLDFYQGHIT
AFLGHNGAGKTTTLSILSGLFPPSGGSAFILGHDVRSSMAAIRPHLGVCP
QYNVLFDMLTVDEHVWFYGRLKGLSAAVVGPEQDRLLQDVGLVSKQSVQT
RHLSGGMQRKLSVAIAFVGGSQVVILDEPTAGVDPASRRGIWELLLKYRE
GRTLILSTHHLDEAELLGDRVAVVAGGRLCCCGSPLFLRRHLGSGYYLTL
VKAVGTPQLLALVQHWVPGARLVEELPHELVLVLPYTGAHDGSFATLFRE
LDTRLAELRLTGYGISDTSLEEIFLKVVEECAADTDWALTRQQLQALLLK
RFLLARRSRRGLFAQIVLPALFVGLALVFSLIVPPFGHYPALRLSPTMYG
AQVSFFSEDAPGDPGRARLLEALLQEAGLEEPPVQHSSHRFSAPEVPAEV
AKVLASGNWTPESPSPACQCSRPGARRLLPDCPAAAGGPPPPQAVTGSGE
VVQNLTGRNLSDFLVKTYPRLVRQGLKTKKWVNEVRYGGFSLGGRDPGLP
SGQELGRSVEELWALLSPLPGGALDRVLKNLTAWAHSLDAQDSLKIWFNN
KGWHSMVAFVNRASNAILRAHLPPGPARHAHSITTLNHPLNLTKEQLSEG
ALMASSVDVLVSICVVFAMSFVPASFTLVLIEERVTRAKHLQLMGGLSPT
LYWLGNFLWDMCNYLVPACIVVLIFLAFQQRAYVAPANLPALLLLLLLYG
WSITPLMYPASFFFSVPSTAYVVLTCINLFIGINGSMATFVLELFSDQKL
QEVSRILKQVFLIFPHFCLGRGLIDMVRNQAMADAFERLQSPLRWEVVGK
NLLAMVIQGPLFLLFTLLLQHRSQEDVARERERVVQGATQGDVLVLRNLT
KVYRGQRMPAVDRLCLGIPPGECFGLLGVNGAGKTSTFRMVTGDTLASRG
EAVLAGHSVAREPSAAHLSMGYCPQSDAIFELLTGREHLELLARLRGVPE
AQVAQTAGSGLARLGLSWYADRPAGTYSGGNKRKLATALALVGDPAVVFL
DEPTTGMDPSARRFLWNSLLAVVREGRSVMLTSHSMEECEALCSRLAIMV
NGRFRCLGSPQHLKGRFAAGHTLTLRVPAARSQPAAAFVAAEFPGAELRE
AHGGRLRFQLPPGGRCALARVFGELAVHGAEHGVEDFSVSQTMLEEVFLY
FSKD
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain8edw Chain A Residue 2223 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8edw Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		F816 A823 K847 T848 T849
Binding residue
(residue number reindexed from 1)		F629 A636 K660 T661 T662
Annotation score4
Enzymatic activity
Enzyme Commision number 7.6.2.1: P-type phospholipid transporter.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0005548 phospholipid transporter activity
GO:0016887 ATP hydrolysis activity
GO:0034188 apolipoprotein A-I receptor activity
GO:0042626 ATPase-coupled transmembrane transporter activity
GO:0090554 phosphatidylcholine floppase activity
GO:0090556 phosphatidylserine floppase activity
GO:0140326 ATPase-coupled intramembrane lipid transporter activity
GO:0140328 floppase activity
GO:0140359 ABC-type transporter activity
Biological Process
GO:0006869 lipid transport
GO:0006909 phagocytosis
GO:0007613 memory
GO:0008542 visual learning
GO:0010875 positive regulation of cholesterol efflux
GO:0018149 peptide cross-linking
GO:0019216 regulation of lipid metabolic process
GO:0033344 cholesterol efflux
GO:0033700 phospholipid efflux
GO:0034205 amyloid-beta formation
GO:0034380 high-density lipoprotein particle assembly
GO:0034504 protein localization to nucleus
GO:0038027 apolipoprotein A-I-mediated signaling pathway
GO:0042985 negative regulation of amyloid precursor protein biosynthetic process
GO:0043409 negative regulation of MAPK cascade
GO:0044857 plasma membrane raft organization
GO:0045332 phospholipid translocation
GO:0045806 negative regulation of endocytosis
GO:0050766 positive regulation of phagocytosis
GO:0055085 transmembrane transport
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0150094 amyloid-beta clearance by cellular catabolic process
GO:1900223 positive regulation of amyloid-beta clearance
GO:1901076 positive regulation of engulfment of apoptotic cell
GO:1902430 negative regulation of amyloid-beta formation
GO:1902991 regulation of amyloid precursor protein catabolic process
GO:1902995 positive regulation of phospholipid efflux
GO:1903898 negative regulation of PERK-mediated unfolded protein response
GO:2000010 positive regulation of protein localization to cell surface
Cellular Component
GO:0000139 Golgi membrane
GO:0001891 phagocytic cup
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0030054 cell junction
GO:0031901 early endosome membrane
GO:0032587 ruffle membrane
GO:0042995 cell projection
GO:0043231 intracellular membrane-bounded organelle
GO:0097386 glial cell projection

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8edw, PDBe:8edw, PDBj:8edw
PDBsum8edw
PubMed36484366
UniProtQ8IZY2|ABCA7_HUMAN Phospholipid-transporting ATPase ABCA7 (Gene Name=ABCA7)

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