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- PDB-1ly3: ANALYSIS OF QUINAZOLINE AND PYRIDOPYRIMIDINE N9-C10 REVERSED BRID... -

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Basic information

Entry
Database: PDB / ID: 1ly3
TitleANALYSIS OF QUINAZOLINE AND PYRIDOPYRIMIDINE N9-C10 REVERSED BRIDGE ANTIFOLATES IN COMPLEX WITH NADP+ AND PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / pcDHFR reversed bridge antifolates
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-COG / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Gangjee, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Analysis of quinazoline and pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductase.
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Gangjee, A.
#1: Journal: Structure / Year: 1994
Title: The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 A resolution
Authors: Champness, J.N. / Achari, A. / Ballantine, S.P. / Bryant, P.K. / Delves, C.J. / Stammers, D.K.
#2: Journal: Biochemistry / Year: 1999
Title: LIGAND-INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+
Authors: Cody, V. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F.
History
DepositionJun 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)25,0013
Polymers23,9191
Non-polymers1,0832
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.373, 43.263, 61.372
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 23918.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pneumocystis carinii (fungus) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL321 / References: UniProt: P16184, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-COG / 2,4-DIAMINO-6-[N-(2',5'-DIMETHOXYBENZYL)-N-METHYLAMINO]QUINAZOLINE


Mass: 339.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: Peg 2000, MES/KCl, KCl, pH 6, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMMES11pH6.0
2100 mM11KCl
38.6 mg/mlprotein11
450 %(w/v)PEG200012
550 mMMES12pH6.0
6100 mM12KCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418,1.5621,1.7321
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 1997 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.56211
31.73211
ReflectionResolution: 1.9→8 Å / Num. all: 13784 / Num. obs: 11539 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.67 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 51
Reflection
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 51 %

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Processing

Software
NameClassification
PROTEINmodel building
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
PROTEINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD2

1cd2


Resolution: 1.9→8 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rwork0.178 --
all-13784 -
obs-11539 88.3 %
Displacement parametersBiso mean: 25.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 73 77 1836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.048
Refinement
*PLUS
Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.055
X-RAY DIFFRACTIONp_plane_restr0.014
X-RAY DIFFRACTIONp_chiral_restr0.171

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