1EKH

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

  • Classification: DNA

  • 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 1.3 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 Fold.Des. 8: 441-452

  • Primary Citation of Related Structures:  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(T ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')A,B8N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDA
Query on DDA

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B
2,6-DIDEOXY-BETA-D-GLUCOSE
2,6-DIDEOXY-BETA-D-MANNOSE
C6 H12 O4
FDWRIIDFYSUTDP-KVTDHHQDSA-N
 Ligand Interaction
1GL
Query on 1GL

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A, B
4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C7 H14 O4
CDRBUGSWTNDUSM-JWXFUTCRSA-N
 Ligand Interaction
ERI
Query on ERI

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B
4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
C9 H16 O5
YJOQPCPEUGDGFS-VHKYIWFCSA-N
 Ligand Interaction
CPH
Query on CPH

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A, 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
None
C21 H24 O9
AOCJXLJIUYHXRS-PKRZCTMMSA-N
 Ligand Interaction
CO
Query on CO

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A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
2GL
Query on 2GL

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A, B
4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C8 H14 O5
VJCDYXNEQSTOMG-JBBNEOJLSA-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 or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-03-08 
  • Released Date: 2000-03-20 
  • Deposition Author(s): Gochin, M.
  • This entry supersedes: 1CQB

Revision History 

  • Version 1.0: 2000-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-28
    Type: Advisory