4KMU

X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin

Structural Biology Knowledgebase: 4KMU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.264

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KMU

Classification: TRANSFERASE / ANTIBIOTIC

Total Structure Weight: 921776.25

Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit alpha A, B, F, G 329 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA pez phs sez b3295 JW3257
DNA-directed RNA polymerase subunit beta C, H 1342 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoB groN nitB rif ron stl stv tabD b3987 JW3950
DNA-directed RNA polymerase subunit beta' D, I 1407 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC tabB b3988 JW3951
DNA-directed RNA polymerase subunit omega E, J 91 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ b3649 JW3624
RNA polymerase sigma factor RpoD X, Y 613 Escherichia coli Gene Name(s): rpoD alt b3067 JW3039

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RFP
Query on RFP

C, H RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D, I ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

D, I MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RFP N/A in BindingDB
N/A in BindingMoad
IC50: 12 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.264
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 184.52 α = 90.00
b = 203.87 β = 90.00
c = 307.87 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-08
  • Released Date: 2013-05-22
  • Deposition author(s): Murakami, K.S.

Revision History

  • 2013-07-03
    Type: Citation | Details: Citation update
  • 2013-05-29
    Type: Citation | Details: Citation update