Structure of PDB 6o9l Chain A Binding Site BS02

Receptor Information

>6o9l Chain A (length=1476) Species: 9606 (Homo sapiens)

DSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMD
PRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRC
VCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEE
MDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDS
QEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLS
VRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKL
LQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRV
DFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG
NSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFN
RQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSL
ETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGE
VMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTH
PDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLE
MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKA
KQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKS
LSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPH
FIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGY
IQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL
KPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERM
REDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKV
VEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFR
LSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHY
AGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILC
RLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISP
WLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRI
RIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYM
HLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTS
NDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRG
HLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIM
LGQLAPAGTGCFDLLLDAEKCKYGME

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: 6o9l Chain A Residue 2002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6o9l Transcription preinitiation complex structure and dynamics provide insight into genetic diseases.
• Resolution: 7.2 Å
• Binding residue (original residue number in PDB): C74 H84
• Binding residue (residue number reindexed from 1): C65 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:6o9l, PDBe:6o9l, PDBj:6o9l
• PDBsum: 6o9l
• PubMed: 31110295
• UniProt: P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)