Structure of PDB 5iy9 Chain A Binding Site BS01

Receptor Information
>5iy9 Chain A (length=1454) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMD
PRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRC
VCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGGH
GGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDE
ECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLA
DIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQK
SGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVP
RSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRF
HPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST
FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN
RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILK
PRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVE
NGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLL
IEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGN
TLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINI
SQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGL
TPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRN
SINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALR
RTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPC
NLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSR
QAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIA
HPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS
KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNP
QSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQI
AEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDD
DVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKAL
QEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERE
LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCS
FEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK
YGME
Ligand information
>5iy9 Chain X (length=83) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gaagggcgcctataaaagggggtgggggcgtttttttttttttttttttt
cgaacactcgagccgagcagacgtgcctacgga
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5iy9 Near-atomic resolution visualization of human transcription promoter opening.
Resolution6.3 Å
Binding residue
(original residue number in PDB)		R190 S1131 K1132 H1417 R1421
Binding residue
(residue number reindexed from 1)		R159 S1100 K1101 H1386 R1390
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:0000287 magnesium ion binding
GO:0001055 RNA polymerase II activity
GO:0003677 DNA 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:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019900 kinase binding
GO:0031625 ubiquitin protein ligase binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
GO:0050436 microfibril binding
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006353 DNA-templated transcription termination
GO:0006355 regulation of DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0033120 positive regulation of RNA splicing
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0031981 nuclear lumen
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5iy9, PDBe:5iy9, PDBj:5iy9
PDBsum5iy9
PubMed27193682
UniProtP24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)

[Back to BioLiP]