Structure of PDB 5iyb Chain B Binding Site BS02

Receptor Information
>5iyb Chain B (length=1165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIV
EDAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMM
PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRST
YCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFA
KKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVAT
LPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAF
VIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCET
KKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK
NLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKA
HQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMV
CPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPA
AIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIRE
REIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVAS
GVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCAS
IIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLV
TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSV
FYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVR
VSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV
TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCE
GITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQ
KISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKI
HSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFE
ASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLF
QELMSMSIAPRMMSV
Ligand information
>5iyb Chain Y (length=75) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cacgtctgctcggctcgagtgttcgatcgcgactgaggacgaacgcgccc
ccacccccttttataggcgcccttc
Receptor-Ligand Complex Structure
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PDB5iyb Near-atomic resolution visualization of human transcription promoter opening.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		R438 D442 K445 Y446 K1052 R1085
Binding residue
(residue number reindexed from 1)		R429 D433 K436 Y437 K1043 R1076
Enzymatic activity
Enzyme Commision number 2.7.7.48: RNA-directed RNA polymerase.
2.7.7.6: DNA-directed RNA polymerase.
3.1.13.-
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0016787 hydrolase 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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5iyb, PDBe:5iyb, PDBj:5iyb
PDBsum5iyb
PubMed27193682
UniProtP30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 (Gene Name=POLR2B)

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