5YTY

Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex

Wu, P.C.Tzeng, S.L.Chang, C.K.Kao, Y.F.Waring, M.J.Hou, M.H.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
echinomycin
D, F
8N/AMutation(s): 0 
N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3')A7unidentified
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3')B7unidentified
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
QUI
Query on QUI

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Download CCD File 
D, F
2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000491
Query on PRD_000491
D,FEchinomycinCyclic depsipeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.222 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 46.362α = 90.00
b = 46.362β = 90.00
c = 48.005γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references, Structure summary