4KN4

X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b

Structural Biology Knowledgebase: 4KN4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.250

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KN4

Classification: TRANSFERASE / ANTIBIOTIC

Total Structure Weight: 921930.44

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta' D, I 1407 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC tabB b3988 JW3951
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit omega E, J 91 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ b3649 JW3624
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase sigma factor RpoD X, Y 613 Escherichia coli Gene Name(s): rpoD alt b3067 JW3039
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1RL
Query on 1RL

C, H Benzoxazinorifamycin-2b
C49 H61 N3 O13
NCYSEZCFZIFVEB-WLRQHHRRSA-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 %)
1RL N/A in BindingDB
N/A in BindingMoad
IC50: 57 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.96 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.250
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 184.68 α = 90.00
b = 203.98 β = 90.00
c = 307.91 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