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- PDB-1yho: Solution structure of human dihydrofolate reductase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1yho
TitleSolution structure of human dihydrofolate reductase complexed with trimethoprim and nadph, 25 structures
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / Inhibitor-Enzyme complex
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsPolshakov, V.I. / Birdsall, B.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Solution structure of human dihydrofolate reductase in its complex with trimethoprim and NADPH.
Authors: Kovalevskaya, N.V. / Smurnyy, Y.D. / Polshakov, V.I. / Birdsall, B. / Bradbury, A.F. / Frenkiel, T. / Feeney, J.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3863
Polymers21,3501
Non-polymers1,0372
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 40structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Dihydrofolate reductase


Mass: 21349.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: Pmt702 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1 / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-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


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
1112D NOESY
1212D COSY
13115N-HSQC
14113C-HSQC
15113C-NOESY-HSQC
16115N-NOESY-HSQC
17115N-REJECTED-NOESY
18113C-REJECTED-NOESY
191HNCA
1101HNCO
1111HN(CO)CA
1121HN(CA)CB
1131CBCA(CO)NH
1141HBHA(CO)NH
1151(H)CCH-TOCSY
NMR detailsText: Backbone assigment was performed using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C, U-98% 15N, 1 mM; NADPH 1mM, trimethoprime 1mM; 50mM phosphate buffer
Solvent system: 50 mm phosphate buffer
Sample conditionsIonic strength: 100 mM KCl / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVarian Inc6.1collection
NMRPipeDelaglio1998-2001processing
CNSBrunger1.1refinement
SparkyGoddard3.5data analysis
ARIA2.0arefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: High temp (1000 K) stage: 30 ps (10000 seps), 1000 -> 0 K cooling (25 K step, 30ps trajectory on each step). 700 steps of final energy optimization.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 25

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