Structure of PDB 4ylo Chain R Binding Site BS02

Receptor Information
>4ylo Chain R (length=497) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN
QVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAENSIDPEL
AREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQF
DYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWF
NAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMS
IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI
SRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED
SHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGID
MNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD
Ligand information
>4ylo Chain 8 (length=49) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gccgcgtcagactcgtaggattatagcatacgtgaggtggatgtcaagt
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ylo Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.
Resolution6.0 Å
Binding residue
(original residue number in PDB)		Y394 W433 Q437 H455 E458 N461 N464 R465 R468 D513 R562 T572 L573 E585 R588
Binding residue
(residue number reindexed from 1)		Y278 W317 Q321 H339 E342 N345 N348 R349 R352 D397 R446 T456 L457 E469 R472
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:4ylo, PDBe:4ylo, PDBj:4ylo
PDBsum4ylo
PubMed25866247
UniProtP00579|RPOD_ECOLI RNA polymerase sigma factor RpoD (Gene Name=rpoD)

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