Structure of PDB 3nal Chain A Binding Site BS01

Receptor Information

>3nal 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: DBK
• InChI: InChI=1S/C34H52O10/c1-8-10-11-12-13-14-15-16-17-18-27(36)42-26-20-32(6,44-23(5)35)24-19-25(41-30(37)21(3)9-2)22(4)28(24)29-34(26,40)33(7,39)31(38)43-29/h9,24-26,29,39-40H,8,10-20H2,1-7H3/b21-9-/t24-,25+,26-,29-,32-,33+,34+/m0/s1
• InChIKey: PTOLDSROGFHZGU-VFCZBPRFSA-N
• SMILES:
  CACTVS 3.370: CCCCCCCCCCCC(=O)O[C@H]1C[C@](C)(OC(C)=O)[C@H]2C[C@@H](OC(=O)\C(C)=C/C)C(=C2[C@@H]3OC(=O)[C@@](C)(O)[C@@]13O)C
  CACTVS 3.370: CCCCCCCCCCCC(=O)O[CH]1C[C](C)(OC(C)=O)[CH]2C[CH](OC(=O)C(C)=CC)C(=C2[CH]3OC(=O)[C](C)(O)[C]13O)C
  OpenEye OEToolkits 1.7.0: CCCCCCCCCCCC(=O)O[C@H]1C[C@]([C@H]2C[C@H](C(=C2[C@H]3[C@]1([C@](C(=O)O3)(C)O)O)C)OC(=O)/C(=C\C)/C)(C)OC(=O)C
  OpenEye OEToolkits 1.7.0: CCCCCCCCCCCC(=O)OC1CC(C2CC(C(=C2C3C1(C(C(=O)O3)(C)O)O)C)OC(=O)C(=CC)C)(C)OC(=O)C
  ACDLabs 12.01: O=C3OC2C1=C(C(OC(=O)\C(=C/C)C)CC1C(OC(=O)C)(CC(OC(=O)CCCCCCCCCCC)C2(O)C3(O)C)C)C
• Formula: C34 H52 O10
• Name: (3S,3aR,4S,6S,6aS,8R,9bS)-6-(acetyloxy)-3,3a-dihydroxy-3,6,9-trimethyl-8-{[(2Z)-2-methylbut-2-enoyl]oxy}-2-oxo-2,3,3a,4,5,6,6a,7,8,9b-decahydroazuleno[4,5-b]furan-4-yl dodecanoate
• ZINC: ZINC000058632934
• PDB chain: 3nal Chain A Residue 997

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nal Critical roles of hydrophobicity and orientation of side chains for inactivation of sarcoplasmic reticulum Ca2+-ATPase with thapsigargin and thapsigargin analogs
• Resolution: 2.65 Å
• Binding residue (original residue number in PDB): L249 L253 E255 F256 Q259 L260 V263 V772 L828 I829 F834
• Binding residue (residue number reindexed from 1): L249 L253 E255 F256 Q259 L260 V263 V772 L828 I829 F834
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.10,Kd=8nM

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:0005515 protein 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:0070588 calcium ion transmembrane transport

Cellular Component

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

External links

• PDB: RCSB:3nal, PDBe:3nal, PDBj:3nal
• PDBsum: 3nal
• PubMed: 20551329
• UniProt: B6CAM1