1EKH

NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2000-03-08 Released: 2000-03-20 
  • Deposition Author(s): Gochin, M.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: MINIMIZED AVERAGED COORDINATES FROM 6 RUNS 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.

Gochin, M.

(2000) Structure 8: 441-452

  • DOI: 10.1016/s0969-2126(00)00124-6
  • Primary Citation of Related Structures:  
    1EKH, 1EKI

  • PubMed Abstract: 
  • The drug chromomycin-A(3) binds to the minor groove of DNA and requires a divalent metal ion for complex formation. (1)H, (31)P and (13)C pseudocontact shifts occurring in the presence of a tightly bound divalent cobalt ion in the complex between d(TTGGCCAA)(2) and chromomycin-A(3) have been used to determine the structure of the complex ...

    The drug chromomycin-A(3) binds to the minor groove of DNA and requires a divalent metal ion for complex formation. (1)H, (31)P and (13)C pseudocontact shifts occurring in the presence of a tightly bound divalent cobalt ion in the complex between d(TTGGCCAA)(2) and chromomycin-A(3) have been used to determine the structure of the complex. The accuracy of the structure was verified by validation with nuclear Overhauser enhancements (NOEs) and J-coupling constants not used in the structure calculation.


    Related Citations: 
    • Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints
      Tu, K., Gochin, M.
      (1999) J Am Chem Soc 121: 9276

    Organizational Affiliation

    Department of Microbiology, University of the Pacific School of Dentistry, San Francisco, CA 94115, USA. miriam@picasso. ucsf.edu



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')A, B8N/A
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranoseC, D 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G63753LU
GlyCosmos:  G63753LU
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-OlivopyranoseE, F 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G79611HT
GlyCosmos:  G79611HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPH
Query on CPH

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B]
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
C21 H24 O9
AOCJXLJIUYHXRS-PKRZCTMMSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
G [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: MINIMIZED AVERAGED COORDINATES FROM 6 RUNS 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2000-03-20 
  • Deposition Author(s): Gochin, M.
  • This entry supersedes: 1CQB

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Advisory
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary