Structure of PDB 3a3y Chain A Binding Site BS06

Receptor Information

>3a3y Chain A (length=992) Species: 7797 (Squalus acanthias)

LDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLT
PPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLY
LGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTIN
AEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEF
SSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGR
TPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVAN
VPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTL
TQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRA
VFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIP
FNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLK
EDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTT
DLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGV
GIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDI
LHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIG
VAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLT
SNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDI
MKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPM
DLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQW
ADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMY
PLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY

Ligand information

• Ligand ID: OBN
• InChI: InChI=1S/C29H44O12/c1-13-22(34)23(35)24(36)25(40-13)41-15-8-19(32)28(12-30)21-17(3-5-27(28,37)9-15)29(38)6-4-16(14-7-20(33)39-11-14)26(29,2)10-18(21)31/h7,13,15-19,21-25,30-32,34-38H,3-6,8-12H2,1-2H3/t13-,15-,16+,17+,18+,19+,21+,22-,23+,24+,25-,26+,27-,28+,29-/m0/s1
• InChIKey: LPMXVESGRSUGHW-HBYQJFLCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]2C[C@H]([C@@]3([C@@H]4[C@@H](CC[C@@]3(C2)O)[C@]5(CC[C@@H]([C@]5(C[C@H]4O)C)C6=CC(=O)OC6)O)CO)O)O)O)O
  ACDLabs 10.04: O=C1OCC(=C1)C4CCC5(O)C3CCC6(O)CC(OC2OC(C(O)C(O)C2O)C)CC(O)C6(CO)C3C(O)CC45C
  CACTVS 3.341: C[C@@H]1O[C@@H](O[C@H]2C[C@@H](O)[C@]3(CO)[C@H]4[C@H](O)C[C@]5(C)[C@H](CC[C@]5(O)[C@@H]4CC[C@]3(O)C2)C6=CC(=O)OC6)[C@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)OC2CC(C3(C4C(CCC3(C2)O)C5(CCC(C5(CC4O)C)C6=CC(=O)OC6)O)CO)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O[CH]2C[CH](O)[C]3(CO)[CH]4[CH](O)C[C]5(C)[CH](CC[C]5(O)[CH]4CC[C]3(O)C2)C6=CC(=O)OC6)[CH](O)[CH](O)[CH]1O
• Formula: C29 H44 O12
• Name: OUABAIN
• ChEMBL: CHEMBL222863
• DrugBank: DB01092
• ZINC: ZINC000008143614
• PDB chain: 3a3y Chain A Residue 6000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3a3y Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): F323 G326 I327 I328 V329 A330 F790 T804
• Binding residue (residue number reindexed from 1): F292 G295 I296 I297 V298 A299 F759 T773
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.15,Kd=0.7nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D376 D717 D721
• Catalytic site (residue number reindexed from 1): D345 D686 D690

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005215 transporter activity
• GO:0005391 P-type sodium:potassium-exchanging transporter activity
• GO:0005524 ATP binding
• GO:0008556 P-type potassium transmembrane transporter activity
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion 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:0036376 sodium ion export across plasma membrane
• GO:1902600 proton transmembrane transport
• GO:1990573 potassium ion import across plasma membrane

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:3a3y, PDBe:3a3y, PDBj:3a3y
• PDBsum: 3a3y
• PubMed: 19666591
• UniProt: Q4H132