Structure of PDB 4yfx Chain J Binding Site BS03

Receptor Information
>4yfx Chain J (length=1155) Species: 331111 (Escherichia coli O139:H28 str. E24377A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQ
CGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR
DCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVA
KTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQ
EQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEK
QVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLH
EQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAI
GVIAAQSIGEPGTQLTGLPRVADLFEARRPKEPAILAEISGIVSFGKETK
GKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDI
LRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAG
SSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRM
RRRAA
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4yfx Chain J Residue 2003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4yfx X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
Resolution3.844 Å
Binding residue
(original residue number in PDB)		C888 C895 C898
Binding residue
(residue number reindexed from 1)		C873 C880 C883
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yfx, PDBe:4yfx, PDBj:4yfx
PDBsum4yfx
PubMed25798859
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]