Structure of PDB 1cy8 Chain A Binding Site BS02

Receptor Information
>1cy8 Chain A (length=563) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPDERGALVNRMGVD
PWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLR
EVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRV
VGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDA
STTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDK
PTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS
TNLSQDAVNMVRGYISDNFGKKYLPESPNQYAHEAIRPSDVNVMAESLKD
MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFD
GWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASL
VKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEE
NFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDP
EEGGMRPNQMVLT
Ligand information
Ligand IDTMP
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-PHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain1cy8 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1cy8 Protein-nucleotide interactions in E. coli DNA topoisomerase I.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		S294 T295 S478 S481 R515 R516
Binding residue
(residue number reindexed from 1)		S270 T271 S446 S449 R483 R484
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E9 S10 D111 D113 E115 Y319 R321 H365
Catalytic site (residue number reindexed from 1) E8 S9 D87 D89 E91 Y295 R297 H333
Enzyme Commision number 5.6.2.1: DNA topoisomerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity
Biological Process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:1cy8, PDBe:1cy8, PDBj:1cy8
PDBsum1cy8
PubMed10504732
UniProtP06612|TOP1_ECOLI DNA topoisomerase 1 (Gene Name=topA)

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