Structure of PDB 6hlq Chain A Binding Site BS06

Receptor Information
>6hlq Chain A (length=1456) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLY
DLALGAFLRNLCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRA
SCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITDISSTLLNEL
KSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRG
KCDNCGMFSPKFRKDGFTKIFETALNEKQITNNRVKGSTYILSTEVKNIL
DTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLPSKLG
EEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLLEDRRVIFSRLMNAFVTI
QNDVNAFIDSTKAQGVPIPGVKQALEKKEGLFRKHMMGKRVNYAARSVIS
PDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQ
IQNEDGSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNKKVYRHIKNRD
VVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYANTGAYNADFDGDEMNM
HFPQNENARAEALNLANTDSQYLTPTSGSPVRGLIQDHISAGVWLTSKDS
FFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIFKPYPLWTGKQIITTV
LLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLCGILDKSQ
YGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATAFTCGMDDLRL
TAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKRLQEILRD
NNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKFPCNSMQAMALSGAKG
SNVNVSQIMCLLGQQALEGRRVPVMVSGKTLPSFKPYETDAMAGGYVKGR
FYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYD
NSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLKKYNPSAL
IEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLAKYNPAKYLGS
VSENFQDKLESFLDKNSKGVNEKKFRALMQLKYMRSLINPGEAVGIIASQ
SVGEPSTQMNVTLGIPRLREIVMTASAAIKTPQMTLPIWNDVSDEQADTF
CKSISKVLLSEVIDKVIVTETTGARSYVIHMRFFDNNEYSEEYDVSKEEL
QNVISNQFIHLLEAAIVKEIKKQKRVEANNNMNKVQRDRQSAIISHHRFI
TKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPHIDRC
VHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEA
ARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQGMETST
SSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGKLNNVGTGSFDVL
AKVPNA
Ligand information
Ligand IDG2P
InChIInChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-30(20,21)3-31(22,23)29-32(24,25)26/h2,4,6-7,10,17-18H,1,3H2,(H,20,21)(H,22,23)(H2,24,25,26)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKeyGXTIEXDFEKYVGY-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(C[P@@](=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O13 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
ChEMBLCHEMBL1232908
DrugBankDB03532
ZINCZINC000016051609
PDB chain6hlq Chain T Residue 3000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hlq The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2.
Resolution3.18 Å
Binding residue
(original residue number in PDB)		R591 P593 N625
Binding residue
(residue number reindexed from 1)		R506 P508 N540
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6hlq, PDBe:6hlq, PDBj:6hlq
PDBsum6hlq
PubMed30913026
UniProtP10964|RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190 (Gene Name=RPA190)

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