Structure of PDB 4yfk Chain J

Receptor sequence

>4yfkJ (length=1152) Species: 331111 (Escherichia coli O139:H28 str. E24377A)

EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRNLLGKRVDYSGRSVITVGPYLRLHQCGL
PKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIRE
HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAV
HVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCV
NAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTS
LKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTV
IFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQF
QSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS
FNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLN
VLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHE
GIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQW
CDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVI
AAQSIGEPGTQLTGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKR
RLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRL
RGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSD
FLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAA
SFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRR
AA

3D structure

• PDB: 4yfk 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.
• Chain: J
• Resolution: 3.571 Å

Enzymatic activity

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	J	A459 D460	A441 D442
BS02	MG	J	D462 D464	D444 D446
BS03	ZN	J	C70 C72 C85	C55 C57 C70
BS04	ZN	J	C888 C895 C898	C870 C877 C880
BS05	4C6	J	L342 G344 A1323 I1352	L324 G326 A1100 I1129

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

External links

• PDB: RCSB:4yfk, PDBe:4yfk, PDBj:4yfk
• PDBsum: 4yfk
• PubMed: 25798859
• UniProt: A7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)