5YTZ

Crystal structure of echinomycin-d(ACGTCGT)2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 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. 46: 7396-7404


Macromolecules

Find similar proteins by: Sequence  |  Structure


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

Download SDF File 
Download CCD File 
D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Download SDF File 
Download CCD File 
D, F
2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-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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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A, B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 41.759α = 90.00
b = 41.759β = 90.00
c = 138.415γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

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
  • Version 1.2: 2018-09-05
    Type: Data collection, Database references