Structure of PDB 5iy9 Chain A Binding Site BS04

Receptor Information

>5iy9 Chain A (length=1454) Species: 9606 (Homo sapiens)

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

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5iy9 Chain A Residue 2003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5iy9 Near-atomic resolution visualization of human transcription promoter opening.
• Resolution: 6.3 Å
• Binding residue (original residue number in PDB): C71 C74 C81 H84
• Binding residue (residue number reindexed from 1): C62 C65 C72 H75
• Annotation score: 1

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

External links

• PDB: RCSB:5iy9, PDBe:5iy9, PDBj:5iy9
• PDBsum: 5iy9
• PubMed: 27193682
• UniProt: P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)