Structure of PDB 5w5y Chain A Binding Site BS03

Receptor Information
>5w5y Chain A (length=1461) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLY
DLALGAFLRNLCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRA
SCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITLDISSTLLNE
LKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSR
GKCDNCGMFSPKFRKDGFTKIFETALNEKQITNNRVKGSTYILSTEVKNI
LDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLPSKL
GEEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIFSRL
MNAFVTIQNDVNAFIDSTKAQKVPIPGVKQALEKKEGLFRKHMMGKRVNY
AARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPD
KWPGATQIQNEDGSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNKKVY
RHIKNRDVVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYANTGAYNADF
DGDEMNMHFPQNENARAEALNLANTDSQYLTPTSGSPVRGLIQDHISAGV
WLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIFKPYPLWTG
KQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLC
GILDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATAFTC
GMDDLRLTAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKR
LQEILRDNNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKFPCNSMQAM
ALSGAKGSNVNVSQIMCLLGQQALEGRRVPVMVSGKTLPSFKPYETDAMA
GGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLE
GVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLK
KYNPSALIEHLDVESALKYSKKTLKYRKKHSPHYKQSVKYDPVLAKYNPA
KYLGSVSENFQDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMRSLIN
PGEAVGIIASQSVGEPSTQMNVTLGIPRLREIVMTASAAIKTPQMTLPIW
NDVSDEQADTFCKSISKVLLSEVIDKVIVTETTAARSYVIHMRFFDNNEY
SEEYDVSKEELQNVISNQFIHLLEAAIVKEIKKQKNMNKVQRDRQSAIIS
HHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIP
HIDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKT
YGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQG
METSTSSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGKLNNVGTG
SFDVLAKVPNA
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5w5y Chain A Residue 1701 [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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PDB5w5y Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		C102 C105 C233 C236
Binding residue
(residue number reindexed from 1)		C102 C105 C203 C206
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001054 RNA polymerase I activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006360 transcription by RNA polymerase I
GO:0006361 transcription initiation at RNA polymerase I promoter
GO:0006362 transcription elongation by RNA polymerase I
GO:0006363 termination of RNA polymerase I transcription
GO:0042254 ribosome biogenesis
GO:0042790 nucleolar large rRNA transcription by RNA polymerase I
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005736 RNA polymerase I complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5w5y, PDBe:5w5y, PDBj:5w5y
PDBsum5w5y
PubMed28623663
UniProtP10964|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 (Gene Name=RPA190)

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