1BP8

4:2:1 mithramycin:Mg++:d(ACCCGGGT)2 complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The three-dimensional structure of the 4:1 mithramycin:d(ACCCGGGT)2 complex: evidence for an interaction between the E saccharides

Keniry, M.A.Owen, E.A.Shafer, R.H.

(2000) Biopolymers 54: 104-114

  • DOI: 10.1002/1097-0282(200008)54:2<104::AID-BIP3>3.0.CO;2-2

  • PubMed Abstract: 
  • Mithramycin and chromomycin, two antitumor drugs, each having an identical aglycone and nearly identical disaccharide and trisaccharide side chains, have differing binding properties to a small oligonucleotide, d(ACCCGGGT)(2) (M. A. Keniry et al., Jo ...

    Mithramycin and chromomycin, two antitumor drugs, each having an identical aglycone and nearly identical disaccharide and trisaccharide side chains, have differing binding properties to a small oligonucleotide, d(ACCCGGGT)(2) (M. A. Keniry et al., Journal of Molecular Biology, 1993, Vol. 231, pp. 753-767). In order to understand the forces that induce four mithramycin molecules to bind to d(ACCCGGGT)(2) instead of two drug molecules in the case of chromomycin, the structure of the 4:2:1 mithramycin: Mg(2+):d(ACCCGGGT)(2) complex was investigated by (1)H-nmr and restrained molecular dynamics. The resulting three-dimensional model showed that in order to accommodate the close approach of one neighboring mithramycin dimer, the inwardly directed CDE saccharide chain of the neighboring mithramycin dimer undergoes a conformational change such that the E saccharide no longer spans the minor groove but reorients so that the hydrophilic face of the E saccharides from the two dimers oppose each other. Two hydrogen bonds are formed between the hydroxyl groups of the two opposing E saccharide groups. The results are interpreted in terms of the differences in stereochemistry and functional group substitutions between mithramycin and chromomycin. A mithramycin dimer is able to self-associate on an oligonucleotide template because it has two hydroxyl groups on the same face of its terminal E saccharide. A chromomycin dimer is unable to self-associate because one of these hydroxyl groups is acetylated and the neighboring hydroxyl group has a stereochemistry that cannot permit close contact of the hydroxyl group with a neighbouring chromomycin dimer.


    Organizational Affiliation

    Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3'A,B8N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDL
Query on DDL

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A, B
2,6-DIDEOXY-BETA-D-GALACTOSE
2,6-DIDEOXY-BETA-D-TALOSE
C6 H12 O4
FDWRIIDFYSUTDP-KAZBKCHUSA-N
 Ligand Interaction
DDA
Query on DDA

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

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A, B
1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-METHYL-ANTHRACENE
C21 H24 O7
XBKVKSRQTHGEJA-LAHPPJGFSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MDA
Query on MDA

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A, B
2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE
C7 H14 O4
YQLFLCVNXSPEKQ-GBNDHIKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance