Structure of PDB 5m3f Chain A Binding Site BS04

Receptor Information
>5m3f Chain A (length=1459) 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
CDNCGMFSPKFRKDGFTKIFETALNEKQITNNRVKGSTYILSTEVKNILD
TVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLPSKLGE
EVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIFSRLMN
AFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKHMMGKR
VNYAARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVIN
GPDKWPGATQIQNEDGSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNK
KVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYANTGAYN
ADFDGDEMNMHFPQNENARAEALNLANTDSQYLTPTSGSPVRGLIQDHIS
AGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIFKPYPL
WTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGA
LLCGILDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATA
FTCGMDDLRLTAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPADDPEL
LKRLQEILRDNNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKFPCNSM
QAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVMVSGKTLPSFKPYETD
AMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTK
QLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYA
LLKKYNPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLA
KYNPAKYLGSVSENFQDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYM
RSLINPGEAVGIIASQSVGEPSTQMANVTLGIPRLREIVMTASAAIKTPQ
MTLPIWNDVSDEQADTFCKSISKVLLSEVIDKVIVTERSYVIHMRFFDNN
EYSEEYDVSKEELQNVISNQFIHLLEAAIVKEIKKQKKVQRDRQSAIISH
HRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPH
IDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTY
GVEAARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQGM
ETSTSSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGKLNNVGTGS
FDVLAKVPN
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5m3f Chain A Residue 3003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5m3f Structure of RNA polymerase I transcribing ribosomal DNA genes.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		D627 D629 D631
Binding residue
(residue number reindexed from 1)		D552 D554 D556
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m3f, PDBe:5m3f, PDBj:5m3f
PDBsum5m3f
PubMed27842382
UniProtP10964|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 (Gene Name=RPA190)

[Back to BioLiP]