Structure of PDB 6k7k Chain A Binding Site BS01

Receptor Information
>6k7k Chain A (length=984) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVRTIFINQPQLTKFCNNHVSTAKYNIITFLPRFLYSQFRRAANSFFLFI
ALLQQIPDVSPTGRYTTLVPLLFILAVAAIKEIIEDIKRHKADNAVNKKQ
TQVLRNGAWEIVHWEKVNVGDIVIIKGKEYIPADTVLLSSSEPQAMCYIE
TSNLDGETNLKIRQGLPATSDIKDVDSLMRISGRIECESPNRHLYDFVGN
IRVPLGADQILLRGAQLRNTQWVHGIVVYTGHDTKLMQNSTSPPLKLSNV
ERITNVQILILFCILIAMSLVCSVGSAIWNRRHSGKDWYLNLNYGGASNF
GLNFLTFIILFNNLIPISLLVTLEVVKFTQAYFINWDLDMHYEPTDTAAM
ARTSNLNEELGQVKYIFSDKTGTLTCNVMQFKKCTIAGVAYGQSSLLENL
QNNHPTAPIICEFLTMMAVCHTAVPERERDKIIYQAASPDEGALVRAAKQ
LNFVFTGRTPDSVIIDSLGQEERYELLNVLEFTSARKRMSVIVRTPSGKL
RLYCKGADTVIYDRLAETSKYKEITLKHLEQFATEGLRTLCFAVAEISES
DFQEWRAVYQRASTSVQNRLLKLEESYELIEKNLQLLGATAIEDKLQDQV
PETIETLMKADIKIWILTGDKQETAINIGHSCKLLKKNMGMIVINFALII
DGKTLKYALTFGVRQYFLDLALSCKAVICCRVSPLQKSEVVEMVKKQVKV
VTLAIGDGANDVSMIQTAHVGVGISGNEGLQAANSSDYSIAQFKYLKNLL
MIHGAWNYNRVSKCILYCFYKNIVLYIIEIWFAFVNGFSGQILFERWCIG
LYNVMFTAMPPLTLGIFERSCRKENMLKYPELYKTSQNALDFNTKVFWVH
CLNGLFHSVILFWFPLKALQYGTAFGNGKTSDYLLLGNFVYTFVVITVCL
KAGLETSYWTWFSHIAIWGSIALWVVFFGIYSSLWPAIPMAPDMSGEAAM
LFSSGVFWMGLLFIPVASLLLDVVYKVIKRTAFK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6k7k Chain A Residue 1201 [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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PDB6k7k Cryo-EM structures capture the transport cycle of the P4-ATPase flippase.
Resolution3.04 Å
Binding residue
(original residue number in PDB)		S490 E493 F534 M541 K557 A559 R590 L592 G671 D672 N789
Binding residue
(residue number reindexed from 1)		S438 E441 F482 M489 K505 A507 R538 L540 G619 D620 N710
Annotation score5
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:0016887 ATP hydrolysis activity
GO:0019829 ATPase-coupled monoatomic cation transmembrane transporter activity
GO:0046872 metal ion binding
GO:0090556 phosphatidylserine floppase activity
GO:0140326 ATPase-coupled intramembrane lipid transporter activity
GO:0140346 phosphatidylserine flippase activity
Biological Process
GO:0006869 lipid transport
GO:0007612 learning
GO:0015914 phospholipid transport
GO:0030335 positive regulation of cell migration
GO:0034220 monoatomic ion transmembrane transport
GO:0045332 phospholipid translocation
GO:0048488 synaptic vesicle endocytosis
GO:0061092 positive regulation of phospholipid translocation
GO:0098655 monoatomic cation transmembrane transport
GO:0140331 aminophospholipid translocation
GO:0150104 transport across blood-brain barrier
Cellular Component
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030672 synaptic vesicle membrane
GO:0031090 organelle membrane
GO:0031410 cytoplasmic vesicle
GO:0035577 azurophil granule membrane
GO:0035579 specific granule membrane
GO:0042584 chromaffin granule membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0098978 glutamatergic synapse
GO:1990531 phospholipid-translocating ATPase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6k7k, PDBe:6k7k, PDBj:6k7k
PDBsum6k7k
PubMed31416931
UniProtQ9Y2Q0|AT8A1_HUMAN Phospholipid-transporting ATPase IA (Gene Name=ATP8A1)

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