Structure of PDB 7vpk Chain A Binding Site BS02

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 IDBEF
InChIInChI=1S/Be.3FH/h;3*1H/q+2;;;/p-3
InChIKeyOGIAHMCCNXDTIE-UHFFFAOYSA-K
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[Be-](F)(F)F
ACDLabs 10.04
CACTVS 3.341		F[Be-](F)F
FormulaBe F3
NameBERYLLIUM TRIFLUORIDE ION
ChEMBL
DrugBank
ZINC
PDB chain7vpk Chain A Residue 1202 [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)		G347 D513 K514 T515 T750
Binding residue
(residue number reindexed from 1)		G267 D433 K434 T435 T654
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
View graph for
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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