4YFK Transcription Transcription Inhibitor date Feb 25, 2015
title Escherichia Coli Rna Polymerase In Complex With Squaramide C
authors V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli O139:H28 (Strain E243 Etec);
Organism_taxid: 331111
Strain: E24377a Etec
Gene: Rpoa, Ece24377a_3778
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 1354003
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, I
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O139:H28 (Strain E243 Etec);
Organism_taxid: 331111
Strain: E24377a Etec
Gene: Rpob, Ece24377a_4528
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 1354003
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, J
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O139:H28 (Strain E243 Etec);
Organism_taxid: 331111
Strain: E24377a Etec
Gene: Rpoc, Ece24377a_4529
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 1354003
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemabc

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, K
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli O139:H28 (Strain E243 Etec);
Organism_taxid: 331111
Strain: E24377a Etec
Gene: Rpoz, Ece24377a_4152
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 1354003
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacycduet-1_ec_rpoz

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F, L
Synonym: Sigma-70
Engineered: Yes

Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rpod, Alt, B3067, Jw3039
Expression_system: Escherichia Coli #1h766
Expression_system_taxid: 1354003
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgemd
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.105 206.438 307.993 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.57 Å
ligand 4C6, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene ECE24377A ; ECE24377A ; ECE24377A ; ECE24377A
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, G


C, I


F, L


J, D


K, E


Primary referenceX-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., Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS, J Med Chem. 2015 Mar 23. PMID:25798859
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2413 Kb) [Save to disk]
  • Biological Unit Coordinates (4yfk.pdb1.gz) 1221 Kb
  • Biological Unit Coordinates (4yfk.pdb2.gz) 1190 Kb
  • LPC: Ligand-Protein Contacts for 4YFK
  • CSU: Contacts of Structural Units for 4YFK
  • Structure Factors (2045 Kb)
  • Retrieve 4YFK in mmCIF format [Save to disk]
  • Re-refined 4yfk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YFK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4YFK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4YFK, from MSDmotif at EBI
  • Fold representative 4yfk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yfk_F] [4yfk] [4yfk_L] [4yfk_B] [4yfk_G] [4yfk_K] [4yfk_J] [4yfk_H] [4yfk_C] [4yfk_I] [4yfk_A] [4yfk_D] [4yfk_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YFK: [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4YFK
  • Community annotation for 4YFK at PDBWiki (http://pdbwiki.org)

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