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- PDB-4hog: Candida glabrata dihydrofolate reductase complexed with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 4hog
TitleCandida glabrata dihydrofolate reductase complexed with NADPH and 5-[3-(2-methoxy-4-phenylphenyl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine (UCP111H)
ComponentsDihydrofolate Reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Antifungal Agents / Candida glabrata / Drug Design / Enzyme Inhibitors / Fungal Proteins / Structure-Activity Relationship / Tetrahydrofolate Dehydrogenase / OXIDOREDUCTASE-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 / 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-18H / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPaulsen, J.L. / Anderson, A.C.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Propargyl-Linked Antifolates are Dual Inhibitors of Candida albicans and Candida glabrata.
Authors: G-Dayanandan, N. / Paulsen, J.L. / Viswanathan, K. / Keshipeddy, S. / Lombardo, M.N. / Zhou, W. / Lamb, K.M. / Sochia, A.E. / Alverson, J.B. / Priestley, N.D. / Wright, D.L. / Anderson, A.C.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate Reductase
B: Dihydrofolate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20410
Polymers52,8552
Non-polymers2,3508
Water3,045169
1
A: Dihydrofolate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6386
Polymers26,4271
Non-polymers1,2105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5674
Polymers26,4271
Non-polymers1,1393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.828, 42.828, 229.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Dihydrofolate Reductase / Strain CBS138 chromosome J complete sequence


Mass: 26427.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata CBS 138 (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: CAGL0J03894g, DHFR / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FPH0
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-18H / 5-[3-(2-methoxy-4-phenylphenyl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine / 5-[(3S)-3-(3-methoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine


Mass: 358.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N4O
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl, Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 26, 2012 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27817 / Num. obs: 27817 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.089 / Χ2: 2.921 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.034.70.19514222.022199.6
2.03-2.077.60.1913201.8271100
2.07-2.117.60.17313992.0521100
2.11-2.157.60.16514302.171100
2.15-2.27.70.15613472.2721100
2.2-2.257.70.14714322.4431100
2.25-2.317.80.14213472.6181100
2.31-2.377.80.13814142.6411100
2.37-2.447.70.1313572.6441100
2.44-2.527.70.12214622.7371100
2.52-2.617.80.11913292.9191100
2.61-2.717.80.11214092.7961100
2.71-2.847.90.10613803.0221100
2.84-2.997.90.09913863.397199.9
2.99-3.177.80.0913923.4621100
3.17-3.427.80.08513953.7531100
3.42-3.767.70.07614034.0241100
3.76-4.317.70.06814063.9541100
4.31-5.437.80.06513913.832199.9
5.43-507.70.06313963.323197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CSE

3cse


Resolution: 2→29.29 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.139 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1391 5 %RANDOM
Rwork0.1852 ---
all0.2373 27724 --
obs0.1878 27724 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 18.7764 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 154 169 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023952
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9995369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59524.086186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86415693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9921524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212968
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 105 -
Rwork0.18 1915 -
all-2020 -
obs--98.87 %

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