Structure of PDB 6k7l Chain A Binding Site BS02

Receptor Information

>6k7l Chain A (length=992) Species: 9606 (Homo sapiens)

EVRTIFINQPAKYNIITFLPRFLYSQFRRAANSFFLFIALLQQIPDVSPT
GRYTTLVPLLFILAVAAIKEIIEDIKRHKADNAVNKKQTQVLRNGAWEIV
HWEKVNVGDIVIIKGKEYIPADTVLLSSSEPQAMCYIETSNLDGETNLKI
RQGLPATSDIKDVDSLMRISGRIECESPNRHLYDFVGNIRVPLGADQILL
RGAQLRNTQWVHGIVVYTGHTSPPLKLSNVERITNVQILILFCILIAMSL
VCSVGSAIWNRRHSGKDWYLNLNYGGASNFGLNFLTFIILFNNLIPISLL
VTLEVVKFTQAYFINWDLDMHYEPTDTAAMARTSNLNEELGQVKYIFSDK
TGTLTCNVMQFKKCTIAGVAYGQFSDSSLLENLQNNHPTAPIICEFLTMM
AVCHTAVPERERDKIIYQAASPDEGALVRAAKQLNFVFTGRTPDSVIIDS
LGQEERYELLNVLEFTSARKRMSVIVRTPSGKLRLYCKGADTVIYDRLAE
TSKYKEITLKHLEQFATEGLRTLCFAVAEISESDFQEWRAVYQRASTSVQ
NRLLKLEESYELIEKNLQLLGATAIEDKLQDQVPETIETLMKADIKIWIL
TGDKQETAINIGHSCKLLKKNMGMIVINDFALIIDGKTLKYALTFGVRQY
FLDLALSCKAVICCRVSPLQKSEVVEMVKKQVKVVTLAIGDGANDVSMIQ
TAHVGVGISGNEGLQAANSSDYSIAQFKYLKNLLMIHGAWNYNRVSKCIL
YCFYKNIVLYIIEIWFAFVNGFSGQILFERWCIGLYNVMFTAMPPLTLGI
FERSCRKENMLKYPELYKTSQNALDFNTKVFWVHCLNGLFHSVILFWFPL
KALQYGTAFGNGKTSDYLLLGNFVYTFVVITVCLKAGLETSYWTWFSHIA
IWGSIALWVVFFGIYSSLWPAIPMAPDMSGEAAMLFSSGVFWMGLLFIPV
ASLLLDVVYKVIKRTAFKLHGYAFSQDENGIVSQSEVIRAYD

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 6k7l Chain A Residue 1802

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k7l Cryo-EM structures capture the transport cycle of the P4-ATPase flippase.
• Resolution: 2.83 Å
• Binding residue (original residue number in PDB): D409 T411 D786
• Binding residue (residue number reindexed from 1): D349 T351 D691
• 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: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

External links

• PDB: RCSB:6k7l, PDBe:6k7l, PDBj:6k7l
• PDBsum: 6k7l
• PubMed: 31416931
• UniProt: Q9Y2Q0|AT8A1_HUMAN Phospholipid-transporting ATPase IA (Gene Name=ATP8A1)