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- PDB-1klk: CRYSTAL STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE... -

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Basic information

Entry
Database: PDB / ID: 1klk
TitleCRYSTAL STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TERNARY COMPLEX WITH PT653 AND NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Structure-based design / antifolate / AIDS / protein-inhibitor complex / NADP / One-carbon metabolism
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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-NDP / Chem-PMD / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Queener, S.F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure-based enzyme inhibitor design: modeling studies and crystal structure analysis of Pneumocystis carinii dihydrofolate reductase ternary complex with PT653 and NADPH.
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Queener, S.F.
#1: Journal: Biochemistry / Year: 2000
Title: Structural Studies on Bioactive Compounds. 30. Crystal Structure and Molecular Modeling Studies on the Pneumocystis carinii Dihydrofolate Reductase Cofactor Complex with TAB, a Highly Selective Antifolate
Authors: Cody, V. / Chan, D. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Laughton, C.A. / Stevens, M.F.G.
#2: Journal: Biochemistry / Year: 1999
Title: Ligand-Induced Conformational Changes in the Crystal Structure 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
DepositionDec 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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)25,0313
Polymers23,9191
Non-polymers1,1132
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.836, 43.138, 59.319
Angle α, β, γ (deg.)90.00, 95.03, 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) / Genus: Rattus / Organ: lung / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P16184, dihydrofolate reductase
#2: Chemical ChemComp-PMD / [N-(2,4-DIAMINOPTERIDIN-6-YL)-METHYL]-DIBENZ[B,F]AZEPINE


Mass: 367.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N7
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 2000MME, KCl, MES, pH 6.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 mg/mlprotein11
220 %(w/v)PEG2000 MME11
3100 mM11KCl
450 mMMES11pH8.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418,1.5621,1.7321
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 1999 / 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: 2.3→25 Å / Num. all: 9597 / Num. obs: 5861 / % possible obs: 61.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 23.4 / Num. unique all: 8889 / Rsym value: 0.234 / % possible all: 89.2
Reflection
*PLUS
Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 640 Random
Rwork0.196 --
all0.196 9597 -
obs0.289 5861 -
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 76 33 1770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.52
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obs% reflection obs (%)
2.3-2.38X-RAY DIFFRACTION41350.2
2.5-2.59X-RAY DIFFRACTION57889.5
Refinement
*PLUS
Highest resolution: 2.4 Å / Num. reflection obs: 5802 / Num. reflection Rfree: 634
Solvent computation
*PLUS
Displacement parameters
*PLUS

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