6CCE

Crystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor Kanglemycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.

Peek, J.Lilic, M.Montiel, D.Milshteyn, A.Woodworth, I.Biggins, J.B.Ternei, M.A.Calle, P.Y.Danziger, M.Warrier, T.Saito, K.Braffman, N.Fay, A.Glickman, M.S.Darst, S.A.Campbell, E.A.Brady, S.F.

(2018) Nat Commun 9: 4147-4147


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase-binding protein RbpA
J
114Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rbpA
Find proteins for A0QZ11 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QZ11
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
350Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for A0QSL8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1169Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P60281 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  P60281
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1317Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for A0QS66 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS66
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
107Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for A0QWT1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QWT1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigA
F
466Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: sigA
Find proteins for A0QW02 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QW02
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
poly(UNK)
G
19N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (57-MER)O57synthetic construct
Small Molecules
Ligands 6 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

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Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
C, D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 130.564α = 90.00
b = 161.583β = 110.73
c = 135.141γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references
  • Version 1.3: 2019-04-24
    Type: Author supporting evidence, Data collection