Structure of PDB 1z5b Chain A Binding Site BS02

Receptor Information
>1z5b Chain A (length=466) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGIL
PNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQ
TRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEP
IIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEF
IFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYT
IKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKY
EDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVE
AGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIE
SDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQ
YLSEKRKEQEAKKKLL
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 chain1z5b Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1z5b Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N42 A46 I81 A89 S96 S97 K98 G109 V112 K113
Binding residue
(residue number reindexed from 1)		N39 A43 I78 A86 S93 S94 K95 G106 V109 K110
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1z5b, PDBe:1z5b, PDBj:1z5b
PDBsum1z5b
PubMed15939019
UniProtO05207|TOP6B_SACSH Type 2 DNA topoisomerase 6 subunit B (Gene Name=top6B)

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