Structure of PDB 8d3u Chain A Binding Site BS01

Receptor Information
>8d3u Chain A (length=971) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EHKMSVEEVCRKYNTDCVQGLTHSKAQEILARDGPNALTPPPTTPEWVKF
CRQLFGGFSILLWIGAILCFLAYGIQAGTEDDPSGDNLYLGIVLAAVVII
TGCFSYYQEAKSSKIMESFKNMVPQQALVIREGEKMQVNAEEVVVGDLVE
IKGGDRVPADLRIISAHGCKVDNSSLTGESEPQTRSPDCTHDNPLETRNI
TFFSTNCVEGTARGVVVATGDRTVMGRIKTPIAIEIEHFIQLITGVAVFL
GVSFFILSLILGYTWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMA
RKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADT
TEDQSGTSFDKSSHTWVALSHIAGLCNRAVFKGGQDNIPVLKRDVAGDAS
ESALLKCIELSSGSVKLMRERNKKVAEIPFNSTNKYQLSIHETEDPNDNR
YLLVMKGAPERILDRCSTILLQGKEQPLDEEMKEAFQNAYLELGGLGERV
LGFCHYYLPEEQFPKGFAFDCDDVNFTTDNLCFVGLMSMIDPPRAAVPDA
VGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPV
SQVNPRDAKACVIHGTDLKDFTSEQIDEILQNHTEIVFARTSPQQKLIIV
EGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDVSKQAADMILLD
DNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLLFIMANIPLPL
GTITILCIDLGTDMVPAISLAYEAAESDIMKRQPRNPRTDKLVNERLISM
AYGQIGMIQALGGFFSYFVILAENGFLPGNLVGIRLNWDDRTVNDLEDSY
GQQWTYEQRKVVEFTCHTAFFVSIVVVQWADLIICKTRRNSVFQQGMKNK
ILIFGLFEETALAAFLSYCPGMDVALRMYPLKPSWWFCAFPYSFLIFVYD
EIRKLILRRNPGGWVEKETYY
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 chain8d3u Chain A Residue 1101 [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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PDB8d3u Structural basis for gating mechanism of the human sodium-potassium pump.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		D440 E443 F472 S474 K477 K498 R541 L543 G608 D609
Binding residue
(residue number reindexed from 1)		D398 E401 F430 S432 K435 K456 R499 L501 G566 D567
Annotation score5
Enzymatic activity
Enzyme Commision number 7.2.2.13: Na(+)/K(+)-exchanging ATPase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0001540 amyloid-beta binding
GO:0005215 transporter activity
GO:0005391 P-type sodium:potassium-exchanging transporter activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008556 P-type potassium transmembrane transporter activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
GO:0051087 protein-folding chaperone binding
GO:1990239 steroid hormone binding
Biological Process
GO:0006813 potassium ion transport
GO:0006814 sodium ion transport
GO:0006883 intracellular sodium ion homeostasis
GO:0010248 establishment or maintenance of transmembrane electrochemical gradient
GO:0030007 intracellular potassium ion homeostasis
GO:0034220 monoatomic ion transmembrane transport
GO:0036376 sodium ion export across plasma membrane
GO:0060075 regulation of resting membrane potential
GO:0071383 cellular response to steroid hormone stimulus
GO:0086064 cell communication by electrical coupling involved in cardiac conduction
GO:1902600 proton transmembrane transport
GO:1903416 response to glycoside
GO:1904646 cellular response to amyloid-beta
GO:1990535 neuron projection maintenance
GO:1990573 potassium ion import across plasma membrane
Cellular Component
GO:0001917 photoreceptor inner segment
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005890 sodium:potassium-exchanging ATPase complex
GO:0016020 membrane
GO:0030424 axon
GO:0031090 organelle membrane
GO:0032809 neuronal cell body membrane
GO:0043025 neuronal cell body
GO:0045202 synapse
GO:0060342 photoreceptor inner segment membrane
GO:0098984 neuron to neuron synapse
GO:1903561 extracellular vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8d3u, PDBe:8d3u, PDBj:8d3u
PDBsum8d3u
PubMed36075933
UniProtP13637|AT1A3_HUMAN Sodium/potassium-transporting ATPase subunit alpha-3 (Gene Name=ATP1A3)

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