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Structure of PDB 8uhd Chain A Binding Site BS05

Receptor Information

>8uhd Chain A (length=1416) Species: 9823 (Sus scrofa)

SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCV
CFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGCGR
YQPRIRRSGLELYAEWKILLSPERVHEIFKRISDEECFVLGMEPRYARPE
WMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQN
GAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGK
EGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTP
FNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKV
ERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADF
DGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR
KFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLII
PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLG
TSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADS
KTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILN
DARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGK
RIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREG
LIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGL
AGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNA
HIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHI
NPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLR
STLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLG
EPATQMTLNKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAK
DILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA
RISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKL
VLRIRIMNSDDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKK
IIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVL
GIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV
NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG
CFDLLLDAEKCKYGME

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: 8uhd Chain A Residue 2002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8uhd Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): C111 F113 C114
• Binding residue (residue number reindexed from 1): C101 F103 C104
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0031981 nuclear lumen
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:8uhd, PDBe:8uhd, PDBj:8uhd
• PDBsum: 8uhd
• PubMed: 38401543
• UniProt: A0A8D1DPV6

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