Structure of PDB 4yfk Chain D

Receptor sequence
>4yfkD (length=1163) Species: 331111 (Escherichia coli O139:H28 str. E24377A) [Search protein sequence]
LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADMIKGKFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWD
ILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD
FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGL
YYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYR
ILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRD
GQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIT
ANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT
EDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPR
NTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIIN
KGEAIGVIAAQSIGEPGTQLTTGGLPRVADLFEARRPKEPAILAEISGIV
SFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDG
PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRK
ATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKAS
LATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY
AYHQDRMRRRAAG
3D structure
PDB4yfk 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.
ChainD
Resolution3.571 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 D A459 D460 A449 D450
BS02 MG D D462 D464 D452 D454
BS03 ZN D C72 C85 C65 C78
BS04 ZN D C814 C888 C895 C898 C804 C878 C885 C888
BS05 4C6 D L342 K345 A1323 V1351 I1352 L332 K335 A1110 V1138 I1139
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:4yfk, PDBe:4yfk, PDBj:4yfk
PDBsum4yfk
PubMed25798859
UniProtA7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]