Structure of PDB 7vpk Chain A Binding Site BS01

Receptor Information
>7vpk Chain A (length=1055) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVRLSGYCGSPWRVIGYHVVVWMMAGIPLLLFRWKPLWGVRLRLRPCNLA
HAETLVIEIRDKEDSSWQLFTVQVQTEAIGRVLRYYLFQGQRYIWIETQQ
AFYQVSLLDHGRSCDDVHRSRHGLSLQDQMVRKAIYGPNVISIPVKSYPQ
LLVDEALNPYYGFQAFSIALWLADHYYWYALCIFLISSISICLSLYKTRK
QSQTLRDMVKLSMRVCVCRPGGEEEWVDSSELVPGDCLVLPQEGGLMPCD
AALVAGECMVNESSLTGESIPVLKTALPEGLGPYCAETHRRHTLFCGTLI
LQARAYVGPHVLAVVTRTGFCTAKGGLVSSILHPRPINFKFYKHSMKFVA
ALSVLALLGTIYSIFILYRNRVPLNEIVIRALDLVTVVVPPALPAAMTVC
TLYAQSRLRRQGIFCIHPLRINLGGKLQLVCFDKTGTLTEDGLDVMGVVP
LKGQAFLPLVPEPRRLPVGPLLRALATCHALSRLQDTPVGDPMDLKMVES
TGWVLEGTQVLAVMRPPLWEPPPVPVSVLHRFPFSSALQRMSVVVAWPGA
TQPEAYVKGSPELVAGLCNPETVPTDFAQMLQSYTAAGYRVVALASKPLP
TVPSLEAAQQLTRDTVEGDLSLLGLLVMRNLLKPQTTPVIQALRRTRIRA
VMVTGDNLQTAVTVARGCGMVAPQEHLIIVHATHPERGQPASLEFLPMES
PSRHLALSGPTFGIIVKHFPKLLPKVLVQGTVFARMAPEQKTELVCELQK
LQYCVGMCGDGANDCGALKAADVGISLSQAEASVVSPFTSSMASIECVPM
VIREGRCSLDTSFSVFKYMALYSLTQFISVLILYTINTNLGDLQFLAIDL
VITTTVAVLMSRTGPALVLGRVRPPGALLSVPVLSSLLLQMVLVTGVQLG
GYFLTLAQPWFVPLNRTVAAPDNLPNYENTVVFSLSSFQYLILAAAVSKG
APFRRPLYTNVPFLVALALLSSVLVGLVLVPGLLQGPLALRNITDTGFKL
LLLGLVTLNFVGAFMLESVLDQCLPACLRRLRPKRASKKRFKQLERELAE
QPWPP
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain7vpk 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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PDB7vpk Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2.
Resolution3.92 Å
Binding residue
(original residue number in PDB)		D513 T515 D878
Binding residue
(residue number reindexed from 1)		D433 T435 D760
Annotation score1
Enzymatic activity
Enzyme Commision number 7.6.2.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005215 transporter activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0008289 lipid binding
GO:0015203 polyamine transmembrane transporter activity
GO:0015417 ABC-type polyamine transporter activity
GO:0015662 P-type ion transporter activity
GO:0016887 ATP hydrolysis activity
GO:0019829 ATPase-coupled monoatomic cation transmembrane transporter activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0070300 phosphatidic acid binding
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding
GO:0140358 P-type transmembrane transporter activity
GO:1903135 cupric ion binding
Biological Process
GO:0006874 intracellular calcium ion homeostasis
GO:0006879 intracellular iron ion homeostasis
GO:0006882 intracellular zinc ion homeostasis
GO:0006914 autophagy
GO:0007041 lysosomal transport
GO:0010628 positive regulation of gene expression
GO:0010821 regulation of mitochondrion organization
GO:0016241 regulation of macroautophagy
GO:0016243 regulation of autophagosome size
GO:0030003 intracellular monoatomic cation homeostasis
GO:0033157 regulation of intracellular protein transport
GO:0034220 monoatomic ion transmembrane transport
GO:0034599 cellular response to oxidative stress
GO:0043523 regulation of neuron apoptotic process
GO:0046777 protein autophosphorylation
GO:0050714 positive regulation of protein secretion
GO:0052548 regulation of endopeptidase activity
GO:0055085 transmembrane transport
GO:0055088 lipid homeostasis
GO:0061462 protein localization to lysosome
GO:0061909 autophagosome-lysosome fusion
GO:0071287 cellular response to manganese ion
GO:0071294 cellular response to zinc ion
GO:0097734 extracellular exosome biogenesis
GO:0098655 monoatomic cation transmembrane transport
GO:1900180 regulation of protein localization to nucleus
GO:1902047 polyamine transmembrane transport
GO:1903146 regulation of autophagy of mitochondrion
GO:1903543 positive regulation of exosomal secretion
GO:1903710 spermine transmembrane transport
GO:1904714 regulation of chaperone-mediated autophagy
GO:1905037 autophagosome organization
GO:1905123 regulation of glucosylceramidase activity
GO:1905165 regulation of lysosomal protein catabolic process
GO:1905166 negative regulation of lysosomal protein catabolic process
GO:1990938 peptidyl-aspartic acid autophosphorylation
GO:2000152 regulation of ubiquitin-specific protease activity
Cellular Component
GO:0000421 autophagosome membrane
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005771 multivesicular body
GO:0005776 autophagosome
GO:0012506 vesicle membrane
GO:0016020 membrane
GO:0030133 transport vesicle
GO:0031902 late endosome membrane
GO:0031982 vesicle
GO:0032585 multivesicular body membrane
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043202 lysosomal lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7vpk, PDBe:7vpk, PDBj:7vpk
PDBsum7vpk
PubMed34798056
UniProtQ9NQ11|AT132_HUMAN Polyamine-transporting ATPase 13A2 (Gene Name=ATP13A2)

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