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- PDB-3qlr: Candida albicans dihydrofolate reductase complexed with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 3qlr
TitleCandida albicans dihydrofolate reductase complexed with NADPH and 6-methyl-5-[(3R)-3-(3,4,5-trimethoxyphenyl)pent-1-yn-1-yl]pyrimidine-2,4-diamine (UCP112A)
ComponentsPutative uncharacterized protein CaJ7.0360
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Antifungal Agents / Candida albicans / Drug Design / Enzyme Inhibitors / Fungal Proteins / Models / Molecular Structure / Structure-Activity Relationship / Tetrahydrofolate Dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Chem-NDP / Chem-QLR / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.149 Å
AuthorsPaulsen, J.L. / Bendel, S.D. / Anderson, A.C.
CitationJournal: Chem.Biol.Drug Des. / Year: 2011
Title: Crystal Structures of Candida albicans Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal the Flexibility of Active Site Loop Residues Critical for Ligand Potency and Selectivity.
Authors: Paulsen, J.L. / Bendel, S.D. / Anderson, A.C.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein CaJ7.0360
B: Putative uncharacterized protein CaJ7.0360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92710
Polymers44,3892
Non-polymers2,5388
Water3,531196
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A: Putative uncharacterized protein CaJ7.0360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5396
Polymers22,1951
Non-polymers1,3445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein CaJ7.0360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3884
Polymers22,1951
Non-polymers1,1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 66.266, 75.888
Angle α, β, γ (deg.)90.000, 92.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative uncharacterized protein CaJ7.0360 / Putative uncharacterized protein DFR1


Mass: 22194.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaJ7.0360, CaO19.12607, CaO19.5142, DFR1, DHFR / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5A5E0, UniProt: P22906*PLUS

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Non-polymers , 5 types, 204 molecules

#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-QLR / 6-methyl-5-[(3R)-3-(3,4,5-trimethoxyphenyl)pent-1-yn-1-yl]pyrimidine-2,4-diamine


Mass: 356.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O3
#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: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, KMES, glycine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2010 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. all: 20375 / Num. obs: 20375 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Χ2: 3.447 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.149-2.193.70.12410183.289198
2.19-2.233.80.10910262.822199.5
2.23-2.273.80.10910033.002199.3
2.27-2.323.70.09510232.737199.3
2.32-2.373.80.09710302.932199.4
2.37-2.423.70.09610103.088199.6
2.42-2.483.80.08910203.028199.4
2.48-2.553.80.08210393.14199.5
2.55-2.623.70.0819883.286199.3
2.62-2.713.80.07510413.237199.6
2.71-2.813.70.07310303.369199.5
2.81-2.923.80.07110163.514199.1
2.92-3.053.70.06910143.753199.6
3.05-3.213.70.06510253.713198.7
3.21-3.413.70.0659974.12198.5
3.41-3.683.70.06210284.444198.5
3.68-4.053.60.06110134.39197.2
4.05-4.633.50.0619944.484195.5
4.63-5.833.80.05710173.56197.1
5.83-503.80.05610623.324198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOE

1aoe


Resolution: 2.149→37.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.239 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1047 5.1 %RANDOM
Rwork0.1755 ---
all0.1789 20375 --
obs0.1789 20375 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.05 Å2 / Biso mean: 21.2418 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.149→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 170 196 3494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223420
X-RAY DIFFRACTIONr_angle_refined_deg1.3242.0334659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75724.085142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98715619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3071522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022488
X-RAY DIFFRACTIONr_nbd_refined0.1920.21459
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.231
X-RAY DIFFRACTIONr_mcbond_it0.5991.52037
X-RAY DIFFRACTIONr_mcangle_it1.01923219
X-RAY DIFFRACTIONr_scbond_it1.40831654
X-RAY DIFFRACTIONr_scangle_it2.0654.51433
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 78 -
Rwork0.186 1425 -
all-1503 -
obs--98.04 %

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