1BZF

NMR SOLUTION STRUCTURE AND DYNAMICS OF THE COMPLEX OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE WITH THE NEW LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE, 22 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 22 
  • Conformers Submitted: 22 
  • Selection Criteria: NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate.

Polshakov, V.I.Birdsall, B.Frenkiel, T.A.Gargaro, A.R.Feeney, J.

(1999) Protein Sci. 8: 467-481

  • DOI: 10.1110/ps.8.3.467
  • Also Cited By: 1LUD

  • PubMed Abstract: 
  • We have determined the three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase and the anticancer drug trimetrexate. Two thousand seventy distance, 345 dihedral angle, and 144 hydrogen bond restraints were o ...

    We have determined the three-dimensional solution structure of the complex of Lactobacillus casei dihydrofolate reductase and the anticancer drug trimetrexate. Two thousand seventy distance, 345 dihedral angle, and 144 hydrogen bond restraints were obtained from analysis of multidimensional NMR spectra recorded for complexes containing 15N-labeled protein. Simulated annealing calculations produced a family of 22 structures fully consistent with the constraints. Several intermolecular protein-ligand NOEs were obtained by using a novel approach monitoring temperature effects of NOE signals resulting from dynamic processes in the bound ligand. At low temperature (5 degrees C) the trimethoxy ring of bound trimetrexate is flipping sufficiently slowly to give narrow signals in slow exchange, which give good NOE cross peaks. At higher temperature these broaden and their NOE cross peaks disappear thus allowing the signals in the lower-temperature spectrum to be identified as NOEs involving ligand protons. The binding site for trimetrexate is well defined and this was compared with the binding sites in related complexes formed with methotrexate and trimethoprim. No major conformational differences were detected between the different complexes. The 2,4-diaminopyrimidine-containing moieties in the three drugs bind essentially in the same binding pocket and the remaining parts of their molecules adapt their conformations such that they can make effective van der Waals interactions with essentially the same set of hydrophobic amino acids, the side-chain orientations and local conformations of which are not greatly changed in the different complexes (similar chi1 and chi2 values).


    Related Citations: 
    • The Solution Structure of the Complex of Lactobacillus Casei Dihydrofolate Reductase with Methotrexate
      Gargaro, A.R.,Soteriou, A.,Frenkiel, T.A.,Bauer, C.J.,Birdsall, B.,Polshakov, V.I.,Barsukov, I.L.,Roberts, G.C.,Feeney, J.
      (1998) J.Mol.Biol. 277: 119


    Organizational Affiliation

    Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
162Lactobacillus caseiMutation(s): 0 
Gene Names: folA (dhfR)
EC: 1.5.1.3
Find proteins for P00381 (Lactobacillus casei)
Go to UniProtKB:  P00381
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMQ
Query on TMQ

Download SDF File 
Download CCD File 
A
TRIMETREXATE
C19 H24 N5 O3
NOYPYLRCIDNJJB-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TMQKd: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 22 
  • Conformers Submitted: 22 
  • Selection Criteria: NO NOE VIOLATION MORE THAN 0.1 ANGSTROM; NO DIHEDRAL ANGLE VIOLATION MORE THAN 3 DEGREES 
  • Olderado: 1BZF Olderado
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance