6CUU

Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic Kanglemycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mode of action of kanglemycin A, a new antibiotic targeting bacterial RNA polymerase

Mosaei, H.Molodtsov, V.Kepplinger, B.Ceccaroni, L.Shin, Y.Morton, S.Wills, C.Clegg, W.Marrs, E.Perry, J.Harbottle, J.Yuzenkova, Y.Errington, J.Allenby, N.Hall, M.J.Murakami, K.S.Zenkin, N.

(2018) Mol.Cell --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
315Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q72I32 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I32
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1119Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q72HM5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HM5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1524Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q72HM6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HM6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q72ID6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72ID6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigA
F
423Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: sigA (rpoD)
Find proteins for Q72L95 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L95
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3')G22Bacillus subtilis
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*CP*TP*CP*TP*GP*AP*TP*GP*CP*A)-3')H27Bacillus subtilis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNG
Query on KNG

Download SDF File 
Download CCD File 
C
Kanglemycin A
4-{(1S)-1-[(1S,2S,12S,16S,17R,18S,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-23-[(2,6-dideoxy-3,4-O-methylidene-beta-D-ribo-hexopyranosyl)oxy]-1,5,6,9,17,19-hexahydroxy-2,4,12,18,20,22-hexamethyl-11-oxo-1,2-dihydro-2,7-(epoxypentadec[1]enoimino)naphtho[2,1-b]furan-16-yl]ethoxy}-3,3-dimethyl-4-oxobutanoic acid
C50 H67 N O19
RKRZBNCHQZDJPK-UAXKWEMASA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 185.221α = 90.00
b = 101.315β = 98.89
c = 294.279γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102851
Leverhulme TrustUnited KingdomPLP-2014-229
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM087350

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references