Structure of PDB 3iyd Chain F Binding Site BS02

Receptor Information
>3iyd Chain F (length=479) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLI
TGFVDPNAEEDLAPTATHVGSELSQEDLDIDPELAREKFAELRAQYVVTR
DTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRT
QERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHD
VSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA
NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE
LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL
DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV
TRERIRQIEAKALRKLRHPSRSEVLRSFL
Ligand information
>3iyd Chain J (length=98) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cttgttatccgctcacaattccacactaattacgagccggaagcataaag
tgtaaagccttttttgcctaaaatgtgatctagatcacatttattgcg
Receptor-Ligand Complex Structure
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PDB3iyd Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
Resolution19.8 Å
Binding residue
(original residue number in PDB)		R397 I457 N461 D570 T572 R588
Binding residue
(residue number reindexed from 1)		R265 I325 N329 D438 T440 R456
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0005515 protein binding
GO:0016987 sigma factor activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:0009408 response to heat
GO:0010468 regulation of gene expression
GO:0045892 negative regulation of DNA-templated transcription
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1903865 sigma factor antagonist complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3iyd, PDBe:3iyd, PDBj:3iyd
PDBsum3iyd
PubMed19903881
UniProtP00579|RPOD_ECOLI RNA polymerase sigma factor RpoD (Gene Name=rpoD)

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