Structure of PDB 7n73 Chain A Binding Site BS01

Receptor Information

>7n73 Chain A (length=1036) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SVRLSGYCGSPWRVIGYHVVVWMMAGIPLLLFRWKPLWGVRLRLRPCNLA
HAETLVIEIWQLFTVQVQTEVLRYYLFQGQRYIWIETQQAFYQVSLLDHG
RSCDDVHRSRHGLSLQDQMVRKAIYGPNVISIPVKSYPQLLVDEALNPYY
GFQAFSIALWLADHYYWYALCIFLISSISICLSLYKTRKQSQTLRDMVKL
SMRVCVCRPGGEEEWVDSSELVPGDCLVLPQEGGLMPCDAALVAGECMVN
ESSLTGESIPVLKTALPEGLGPYCAETHRRHTLFCGTLILQARAYVGPHV
LAVVTRTGFCTAKGGLVSSILHPRPINFKFYKHSMKFVAALSVLALLGTI
YSIFILYRNRVPLNEIVIRALDLVTVVVPPALPAAMTVCTLYAQSRLRRQ
GIFCIHPLRINLGGKLQLVCFDKTGTLTEDGLDVMGVVPLKGQAFLPLVP
EPRRLPVGPLLRALATCHALSRLQDTPVGDPMDLKMVESTGWVLEDSAFG
TQVPVPVSVLHRFPFSSALQRMSVVVAWPGATQPEAYVKGSPELVAGLCN
PETVPTDFAQMLQSYTAAGYRVVALASKPLPTVPSLEAAQQLTRDTVEGD
LSLLGLLVMRNLLKPQTTPVIQALRRTRIRAVMVTGDNLQTAVTVARGCG
MVAPQEHLIIVHATHPERGQPASLEFLPMESRSRHLALSGPTFGIIVKHF
PKLLPKVLVQGTVFARMAPEQKTELVCELQKLQYCVGMCGDGANDCGALK
AADVGISLSQAEASVVSPFTSSMASIECVPMVIREGRCSLDTSFSVFKYM
ALYSLTQFISVLILYTINTNLGDLQFLAIDLVITTTVAVLMSRTGPALVL
GRVRPPGALLSVPVLSSLLLQMVLVTGVQLGGYFLTLAQPWFVPLNRTVA
APDNLPNYENTVVFSLSSFQYLILAAAVSKGAPFRRPLYTNVPFLVALAL
LSSVLVGLVLVPGLLQGPLALRNITDTGFKLLLLGLVTLNFVGAFMLESV
LDQCLPACLRRLRPKRASKKRFKQLERELAEQPWPP

Ligand information

Ligand ID

ADP

InChI

InChI=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

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

7n73 Chain A Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7n73 Structural basis of polyamine transport by human ATP13A2 (PARK9).
Resolution	2.9 Å
Binding residue (original residue number in PDB)	T510 D566 M568 D569 F625 S627 Q630 M632 K649 R681 V683 G746 D747 R848 N876
Binding residue (residue number reindexed from 1)	T424 D480 M482 D483 F515 S517 Q520 M522 K539 R571 V573 G636 D637 R716 N744
Annotation score	5

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

View graph for
Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7n73, PDBe:7n73, PDBj:7n73
PDBsum	7n73
PubMed	34715013
UniProt	Q9NQ11\|AT132_HUMAN Polyamine-transporting ATPase 13A2 (Gene Name=ATP13A2)

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