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- PDB-1lud: SOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIM... -

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Basic information

Entry
Database: PDB / ID: 1lud
TitleSOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIMETHOPRIM AND NADPH, 24 STRUCTURES
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / DHFR / INHIBITOR-ENZYME COMPLEX
Function / homology
Function and homology information


response to methotrexate / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Chem-TRR / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Smirnov, E.G. / Birdsall, B. / Kelly, G. / Feeney, J.
Citation
Journal: J.Biomol.Nmr / Year: 2002
Title: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH
Authors: Polshakov, V.I. / Smirnov, E.G. / Birdsall, B. / Kelly, G. / Feeney, J.
#1: Journal: J.Mol.Struct. / Year: 2002
Title: Towards understanding the origins of the different specificities of binding the reduced (NADPH) and oxydised (NADP+) forms of nicotinamide adenine dinucleotide phosphate coenzyme to dihydrofolate reductase
Authors: Polshakov, V.I. / Biekofsky, R.R. / Birdsall, B. / Feeney, J.
#2: Journal: Biochemistry / Year: 1999
Title: Characterization of rates of ring-flipping in trimethoprim in its ternary complexes with Lactobacillus casei dihydrofolate reductase and coenzyme analogues
Authors: Polshakov, V.I. / Birdsall, B. / Feeney, J.
#3: Journal: Protein Sci. / Year: 1999
Title: Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate
Authors: Polshakov, V.I. / Birdsall, B. / Frenkiel, T.A. / Gargaro, A.R. / Feeney, J.
#4: Journal: J.Mol.Biol. / Year: 1998
Title: The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate
Authors: Gargaro, A.R. / Soteriou, A. / Frenkiel, T.A. / Bauer, C.J. / Birdsall, B. / Polshakov, V.I. / Barsukov, I.L. / Roberts, G.C.K. / Feeney, J.
History
DepositionMay 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3683
Polymers18,3321
Non-polymers1,0372
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 32structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein DIHYDROFOLATE REDUCTASE /


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1 / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-TRR / 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM / Trimethoprim


Mass: 291.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N4O3 / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1313D 15N-separated ROESY
1412D N15-rejected NOESY
1522D NOESY
162DQF-COSY
173J-MODULATED N15, H1-HSQC
184J-MODULATED N15, H1-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer90% H2O/10% D2O
23 mM DHFR/TMP/NADPH, 50 mM phosphate buffer100% D2O
30.5mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% DMPC/DHPC (3:1)90% H2O/10% D2O
40.25mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% C12E5/hexanol90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYVarianUNITY6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe1998-2001Delaglioprocessing
CNS0.9Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 10 ps at 1000K, 40 ps cooling from 1000 to 0K, 1000 steps of EM
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 32 / Conformers submitted total number: 24

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