Structure of PDB 5m3m Chain A Binding Site BS01

Receptor Information
>5m3m Chain A (length=1462) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLY
DLALGAFLRNLCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRA
SCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITLSSTLLNELK
SKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGK
CDNCGMFSPKFRKDGFTKIFETALNEKQITNNRVKGFIRQDSTYILSTEV
KNILDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLP
SKLGEEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIF
SRLMNAFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKH
MMGKRVNYAARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELR
QAVINGPDKWPGATQIQNEDGSLVSLIGMSVEQRKALANQLLTPSSNVST
HTLNKKVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYAN
TGAYNADFDGDEMNMHFPQNENARAEALNLANTDSQYLTPTSGSPVRGLI
QDHISAGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIF
KPYPLWTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVL
FKDGALLCGILDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNY
ITATAFTCGMDDLRLTAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPA
DDPELLKRLQEILRDNNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKF
PCNSMQAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVMVSGKTLPSFK
PYETDAMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAGYLQRCLTKQ
LEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYAL
LKKYNPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLAK
YNPAKYLGSVSENFQDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMR
SLINPGEAVGIIASQSVGEPSTQMTLNTFANVTLGIPRLREIVMTASAAI
KTPQMTLPIWNDVSDEQADTFCKSISKVLLSEVIDKVIVTETTAARSYVI
HMRFFDNNEYSEEYDVSKEELQNVISNQFIHLLEAAIVKEIKKQKKVQRD
RQSAIISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRK
SIIRQIPHIDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSND
VAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTY
LAFNRQGMETSTSSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGK
LNNVGTGSFDVL
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 chain5m3m Chain A Residue 3001 [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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PDB5m3m Structure of RNA polymerase I transcribing ribosomal DNA genes.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		C65 L67 C72 P73
Binding residue
(residue number reindexed from 1)		C65 L67 C72 P73
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:5m3m, PDBe:5m3m, PDBj:5m3m
PDBsum5m3m
PubMed27842382
UniProtP10964|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 (Gene Name=RPA190)

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