Structure of PDB 5j5p Chain B Binding Site BS02

Receptor Information
>5j5p Chain B (length=396) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVD
EALSGFGDRIDVTINKDGSLTVQDHGRGMPTGMHAMGIPTVEVIFTILHA
GGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGK
PVTTLKKIGTAPKSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLL
KNVTLSLTDKRTDEAIEFHYENGVQDFVSYLNEDKEILTPVLYFEGEDNG
FQVEVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITKVMNDYARK
TGLLKEKDKNLEGSDYREGLAAVLSILVPEEHLQFEGQTKDKLGSPLARP
VVDGIVADKLTFFLMENGELASNLIRKAIKARDAREAARKARDESR
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5j5p Chain B Residue 501 [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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PDB5j5p Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		N51 E55 M83 I98 G105 G106 K107 Y113 G118 L119 H120 G121 V122 G123 S124 T172 K344
Binding residue
(residue number reindexed from 1)		N47 E51 M79 I94 G101 G102 K103 Y109 G114 L115 H116 G117 V118 G119 S120 T168 K340
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
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
View graph for
Biological Process
External links
PDB RCSB:5j5p, PDBe:5j5p, PDBj:5j5p
PDBsum5j5p
PubMed29968711
UniProtQ59961|PARE_STRPN DNA topoisomerase 4 subunit B (Gene Name=parE)

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