Structure of PDB 5oik Chain B Binding Site BS03

Receptor Information
>5oik Chain B (length=1147) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPI
DLQPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVD
ITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNEC
PLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLEN
SSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALG
FVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAK
PGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAAL
GRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGK
DFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFAS
TLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLA
LMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIH
KDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLI
VEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAM
TPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSA
MGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGIN
SIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEE
VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENE
DELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVR
IPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT
IGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEV
LYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEG
RSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAI
ANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV
Ligand information
>5oik Chain T (length=43) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gatcaagctcaagtacttaagcctggtctatactagtactgcc
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5oik Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		G1077 R1078 R1085 M1089
Binding residue
(residue number reindexed from 1)		G1050 R1051 R1058 M1062
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: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:0016787 hydrolase activity
GO:0032549 ribonucleoside binding
GO:0046872 metal ion binding
GO:0071667 DNA/RNA hybrid 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5oik, PDBe:5oik, PDBj:5oik
PDBsum5oik
PubMed28892040
UniProtA5PJW8|RPB2_BOVIN DNA-directed RNA polymerase II subunit RPB2 (Gene Name=POLR2B)

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