Structure of PDB 6pcm Chain B Binding Site BS01

Receptor Information
>6pcm Chain B (length=783) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVRRLVIVESPTKARKIAGYLGSNYVVESSRGHIRDLPRNAADVPAKFKS
EPWARLGVNVDQNFEPLYIVSPEKKSTVTELKGLLKDVDELYLATDGDRE
GEAIAWHLLETLKPRVPVKRMVFHEITEPAIRNAAENPRDLDIALVDAQE
TRRILDRLYGYEVSPVLWKKVAPKLSAGRVQSVATRIIVQRERERMAFHS
ASYWDVTAELDASVSDPSASPPKFTAKLNTVDGRRVATGRDFDSLGQLKR
PDEVLVLDEASAGALASGLRGAQLAVTSVEQKPYTRRPYAPFMTSTLQQE
AARKLRFSSERTMSIAQRLYENGYITYMRTDSTTLSESAINAARTQARQL
YGEEYVHPSPRQYTRKVNAQEAHEAIRPAGDVFQTPGQLHSALDTDEFRL
YELIWQRTVASQMADARGTTLSLRIGGSASSGEQVVFNASGRTITFPGFL
KAYVSRLPNLTQGQRVDAADLSADGHQTSPPARYTEASLIKALEELGIGR
PSTYSSIIKTIQDRGYVQKKGSALVPSWVAFAVVGLLEQHFGRLVDYDFT
AAMEDELDEIANGQEQRTNWLNNFYFGGEHGVEGSIARAGGLKQLVGGNL
EGIDAREVNSIKVFDDSEGRPVYVRVGRNGPYLERMVDDPDNQKPQRANL
KEDLTPDELTPELAEKLFATPQEGRSLGIDPETGHEIVAKDGRFGPYVTE
VLPETGPKPRTGSLFRSMDLETVTLEDALKLLSLPRVTTNEEITAQNGRY
GPYLKRGTDSRSLATEDQIFTITLDEALKIYAE
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6pcm Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.
Resolution3.107 Å
Binding residue
(original residue number in PDB)		W180 K181 G723 R724 F725 G726 P727 Y728 T762 G804 R805 Y806 Y809 S816 R817 S818
Binding residue
(residue number reindexed from 1)		W168 K169 G692 R693 F694 G695 P696 Y697 T711 G748 R749 Y750 Y753 S760 R761 S762
Enzymatic activity
Catalytic site (original residue number in PDB) E21 S22 D108 D110 Y339 R341
Catalytic site (residue number reindexed from 1) E9 S10 D96 D98 Y327 R329
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
GO:0046872 metal ion binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pcm, PDBe:6pcm, PDBj:6pcm
PDBsum6pcm
PubMed32232337
UniProtA0R5D9|TOP1_MYCS2 DNA topoisomerase 1 (Gene Name=topA)

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