Structure of PDB 1z59 Chain A Binding Site BS01

Receptor Information
>1z59 Chain A (length=462) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKI
TIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMY
GLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVER
GSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDP
EGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFL
VNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRS
PSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAF
GGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQ
MVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEK
RKEQEAKKKLLA
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 chain1z59 Chain A Residue 2001 [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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PDB1z59 Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		N42 A46 I81 A89 V112
Binding residue
(residue number reindexed from 1)		N34 A38 I73 A81 V104
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:1z59, PDBe:1z59, PDBj:1z59
PDBsum1z59
PubMed15939019
UniProtO05207|TOP6B_SACSH Type 2 DNA topoisomerase 6 subunit B (Gene Name=top6B)

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