Structure of PDB 2yfy Chain A Binding Site BS01

Receptor Information

>2yfy Chain A (length=994) Species: 9986 (Oryctolagus cuniculus)

MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLW
ELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIA
NAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDI
VEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAV
NQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQ
QKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAV
ALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICS
DKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDK
PIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVE
KMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSP
AKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIK
EWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML
DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVAD
RAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAM
TGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEG
RAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTD
GLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVG
AAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMA
LSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYV
DPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Ligand information

• Ligand ID: 9TN
• InChI: InChI=1S/C30H44O11/c1-8-10-11-12-13-14-20(33)38-24-22-21(17(4)23(24)39-26(34)16(3)9-2)25-30(37,29(7,36)27(35)40-25)19(32)15-28(22,6)41-18(5)31/h9,19,22-25,32,36-37H,8,10-15H2,1-7H3/b16-9+/t19-,22+,23-,24-,25-,28-,29+,30+/m0/s1
• InChIKey: UBPDDZPGODTCDF-NPAVTDDVSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCC(=O)OC1C2C(=C(C1OC(=O)C(=CC)C)C)C3C(C(CC2(C)OC(=O)C)O)(C(C(=O)O3)(C)O)O
  OpenEye OEToolkits 2.0.7: CCCCCCCC(=O)O[C@H]1[C@H]2C(=C([C@@H]1OC(=O)/C(=C/C)/C)C)[C@H]3[C@]([C@H](C[C@]2(C)OC(=O)C)O)([C@](C(=O)O3)(C)O)O
  CACTVS 3.385: CCCCCCCC(=O)O[C@@H]1[C@@H](OC(=O)C(/C)=C/C)C(=C2[C@@H]3OC(=O)[C@@](C)(O)[C@@]3(O)[C@@H](O)C[C@](C)(OC(C)=O)[C@@H]12)C
  CACTVS 3.385: CCCCCCCC(=O)O[CH]1[CH](OC(=O)C(C)=CC)C(=C2[CH]3OC(=O)[C](C)(O)[C]3(O)[CH](O)C[C](C)(OC(C)=O)[CH]12)C
• Formula: C30 H44 O11
• Name: DEBUTANOYL THAPSIGARGIN
• ZINC: ZINC000066166286
• PDB chain: 2yfy Chain A Residue 1995

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yfy Mutual Adaptation of a Membrane Protein and its Lipid Bilayer During Conformational Changes.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): L260 V263 I765 N768 V769 V772 I829 F834 Y837 M838
• Binding residue (residue number reindexed from 1): L260 V263 I765 N768 V769 V772 I829 F834 Y837 M838
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D351 D703 D707
• Catalytic site (residue number reindexed from 1): D351 D703 D707
• Enzyme Commision number: 7.2.2.10: P-type Ca(2+) transporter.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0005215 transporter activity
• GO:0005388 P-type calcium transporter activity
• GO:0005509 calcium ion binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006816 calcium ion transport
• GO:0006874 intracellular calcium ion homeostasis
• GO:0031448 positive regulation of fast-twitch skeletal muscle fiber contraction
• GO:0070588 calcium ion transmembrane transport
• GO:0106134 positive regulation of cardiac muscle cell contraction
• GO:1901896 positive regulation of ATPase-coupled calcium transmembrane transporter activity
• GO:1902082 positive regulation of calcium ion import into sarcoplasmic reticulum
• GO:1990036 calcium ion import into sarcoplasmic reticulum

Cellular Component

• GO:0016020 membrane
• GO:0016529 sarcoplasmic reticulum
• GO:0033017 sarcoplasmic reticulum membrane

External links

• PDB: RCSB:2yfy, PDBe:2yfy, PDBj:2yfy
• PDBsum: 2yfy
• PubMed: 21556058
• UniProt: P04191|AT2A1_RABIT Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (Gene Name=ATP2A1)