Structure of PDB 1twc Chain B Binding Site BS02

Receptor Information
>1twc Chain B (length=1091) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDS
TLIEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKR
TYEKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEK
VLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYG
REGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQM
LEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEF
LPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAG
PLLAQLFKTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGA
GVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQAC
GLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVN
GVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRV
YRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEY
IDAEEEESILIAMQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGV
AASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQK
PLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF
RSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP
GVRVSGEDVIIGKTTSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPGLRFGEM
ERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECK
GCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF
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
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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)
R766 Q986 K987 S1019 R1020
Binding residue
(residue number reindexed from 1)
R665 Q869 K870 S902 R903
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D736
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:0003729 mRNA 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:0032549 ribonucleoside binding
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:1twc, PDBe:1twc, PDBj:1twc
PDBsum1twc
PubMed15537538
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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