1PFE

Echinomycin-(gcgtacgc)2 complex

Structural Biology Knowledgebase: 1PFE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Observed: 0.146

Literature

Macromolecules
Sequence Display for 1PFE

Classification: DNA / ANTIBIOTIC

Total Structure Weight: 3620.40


Macromolecule Entities
Molecule Chains Length Organism Details
ECHINOMYCIN B 8 Streptomyces echinatus Mutation: X3X, X7X
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3' A 8 synthetic

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

B 2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000491
Query on PRD_000491
B Echinomycin Cyclic depsipeptide /
Antibiotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Observed: 0.146
  • Space Group: P 63 2 2

Unit Cell:

Length (Å) Angle (°)
a = 39.37 α = 90.00
b = 39.37 β = 90.00
c = 79.73 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-26
  • Released Date: 2004-06-08
  • Deposition author(s): Cuesta-Seijo, J.A.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-27
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-27
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-27
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4