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- PDB-6pr8: S. aureus dihydrofoate reductase co-crystallized with 3,5-dimethy... -

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Basic information

Entry
Database: PDB / ID: 6pr8
TitleS. aureus dihydrofoate reductase co-crystallized with 3,5-dimethylphenyl-dihydropthalazine inhibitor and NADP(H)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/INHIBITOR / DIHYDROFOLATE REDUCTASE / OXIDOREDUCTASE-INHIBITOR COMPLEX
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 / cytosol
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-OWJ / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBourne, C.R. / Thomas, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI090685-01 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase.
Authors: Muddala, N.P. / White, J.C. / Nammalwar, B. / Pratt, I. / Thomas, L.M. / Bunce, R.A. / Berlin, K.D. / Bourne, C.R.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,0885
Polymers18,6111
Non-polymers1,4764
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 78.890, 107.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18611.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-OWJ / (2E)-3-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(3,5-dimethylphenyl)phthalazin-2(1H)-yl]prop-2-en-1-one


Mass: 548.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H32N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% PEG6000, 0.1M MES, 0.15M NaAcetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 2, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→23.3 Å / Num. obs: 13486 / % possible obs: 97.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 18.71 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.4
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.303 / Num. unique obs: 1301

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M08

3m08


Resolution: 2.01→23.292 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.88
RfactorNum. reflection% reflection
Rfree0.2308 670 5.02 %
Rwork0.1771 --
obs0.1796 13359 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.87 Å2 / Biso mean: 20.93 Å2 / Biso min: 5.32 Å2
Refinement stepCycle: final / Resolution: 2.01→23.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 101 169 1580
Biso mean--28.79 28.52 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151475
X-RAY DIFFRACTIONf_angle_d1.7692015
X-RAY DIFFRACTIONf_chiral_restr0.241221
X-RAY DIFFRACTIONf_plane_restr0.005246
X-RAY DIFFRACTIONf_dihedral_angle_d25.531586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.1630.28051440.2035240795
2.163-2.38050.291260.2084242794
2.3805-2.72450.25541440.1924250297
2.7245-3.43080.2061230.1751258898
3.4308-23.2920.1971330.1544276599

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