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- PDB-1hfr: COMPARISON OF TERNARY CRYSTAL COMPLEXES OF HUMAN DIHYDROFOLATE RE... -

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Basic information

Entry
Database: PDB / ID: 1hfr
TitleCOMPARISON OF TERNARY CRYSTAL COMPLEXES OF HUMAN DIHYDROFOLATE REDUCTASE WITH NADPH AND A CLASSICAL ANTITUMOR FUROPYRIMDINE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ONE-CARBON METABOLISM
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-MOT / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Blakley, R.L. / Gangjee, A.
Citation
Journal: Anti-Cancer Drug Des. / Year: 1998
Title: Comparison of ternary crystal complexes of F31 variants of human dihydrofolate reductase with NADPH and a classical antitumor furopyrimidine.
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Blakley, R.L. / Gangjee, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Comparison of Ternary Complexes of Pneumocystis Carinii and Wild-Type Human Dihydrofolate Reductase with a Novel Classical Antitumor Furo[2,3-D]Pyrimidine Antifolate
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Devraj, R. / Queener, S.F. / Blakley, R.L.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Methotrexate-Resistant Variants of Human Dihydrofolate Reductase with Substitutions of Leucine 22. Kinetics, Crystallography, and Potential as Selectable Markers
Authors: Lewis, W.S. / Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Chunduru, S.K. / Spencer, H.T. / Appleman, J.R. / Blakley, R.L.
#3: Journal: J.Biol.Chem. / Year: 1994
Title: Methotrexate-Resistant Variants of Human Dihydrofolate Reductase. Effects of Phe31 Substitutions
Authors: Chunduru, S.K. / Cody, V. / Luft, J.R. / Pangborn, W. / Appleman, J.R. / Blakley, R.L.
#4: Journal: Anti-Cancer Drug Des. / Year: 1992
Title: Crystal Structure Determination at 2.3 A of Recombinant Human Dihydrofolate Reductase Ternary Complex with Nadph and Methotrexate-Gamma-Tetrazole
Authors: Cody, V. / Luft, J.R. / Ciszak, E. / Kalman, T.I. / Freisheim, J.H.
History
DepositionNov 4, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2013Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers21,3501
Non-polymers1,1882
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.900, 86.900, 77.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / DHFR


Mass: 21349.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NADPH AND FURO[2,3D]FUROPYRIMIDINE / Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / Strain (production host): JM107 / 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-MOT / N-[4-[(2,4-DIAMINOFURO[2,3D]PYRIMIDIN-5-YL)METHYL]METHYLAMINO]-BENZOYL]-L-GLUTAMATE


Mass: 442.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 48 %

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→8 Å / Num. obs: 10428 / % possible obs: 84.7 % / Observed criterion σ(I): 2 / Redundancy: 3.09 % / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
PROFFTrefinement
R-AXISIIdata reduction
RefinementRfactor Rwork: 0.1995 / Highest resolution: 2.1 Å
Displacement parametersBiso mean: 24.79 Å2
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 80 35 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.0660.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.070.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.061.5
X-RAY DIFFRACTIONp_mcangle_it1.5861.5
X-RAY DIFFRACTIONp_scbond_it0.9361
X-RAY DIFFRACTIONp_scangle_it1.5271.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.240.15
X-RAY DIFFRACTIONp_singtor_nbd0.2430.5
X-RAY DIFFRACTIONp_multtor_nbd0.2710.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.270.5
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.620
X-RAY DIFFRACTIONp_special_tor

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