Structure of PDB 5iyd Chain B Binding Site BS04

Receptor Information
>5iyd 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
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5iyd Chain B Residue 1201 [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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PDB5iyd Near-atomic resolution visualization of human transcription promoter opening.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		C1137 R1138
Binding residue
(residue number reindexed from 1)		C1128 R1129
Annotation score1
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5iyd, PDBe:5iyd, PDBj:5iyd
PDBsum5iyd
PubMed27193682
UniProtP30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 (Gene Name=POLR2B)

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