Structure of PDB 1twc Chain A Binding Site BS04

Receptor Information
>1twc Chain A (length=1351) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVL
STEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPDLTF
KLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDSIRARLDFS
ARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNE
HPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQP
SLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETR
AELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLN
MLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLL
SPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGN
IQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQ
ANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVM
AGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKG
FVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDI
MVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYR
VDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFV
DGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLL
VLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSN
IEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVA
KNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDP
RSTVIPEDEEIIQLHLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTF
KNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIE
RVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTN
SFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTTVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEES
L
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain1twc Chain B Residue 3008 [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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PDB1twc Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D481 D483 K752
Binding residue
(residue number reindexed from 1)		D433 D435 K704
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D433 D435 D437
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent 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
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1twc, PDBe:1twc, PDBj:1twc
PDBsum1twc
PubMed15537538
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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