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- PDB-9y7q: Crystal structure of Candida auris dihydrofolate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 9y7q
TitleCrystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1051 (S-form) and NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / 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 conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
: / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandidozyma auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsErlandsen, H. / Wright, D. / Krucinska, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structural and biological evaluation of non-classical antifolates as antifungal drug candidates targeting Candia auris dihydrofolate reductase.
Authors: Erlandsen, H. / Wright, D. / Krucinska, J.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2736
Polymers48,0952
Non-polymers2,1784
Water73941
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1363
Polymers24,0481
Non-polymers1,0892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1363
Polymers24,0481
Non-polymers1,0892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.088, 69.819, 112.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase


Mass: 24047.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidozyma auris (fungus) / Gene: QG37_02791 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L0P1H8, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1CTC / 6-ethyl-5-[(3S)-3-(6-phenylpyridin-3-yl)but-1-yn-1-yl]pyrimidine-2,4-diamine


Mass: 343.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 28% PEG 3,350 0.2M LiSO4 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 2.42→32.96 Å / Num. obs: 19895 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.101 / Net I/σ(I): 8.5
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2053 / CC1/2: 0.386 / Rpim(I) all: 0.683 / Rrim(I) all: 0.965 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→32.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.935 / SU B: 24.875 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24393 1022 5.1 %RANDOM
Rwork0.15997 ---
obs0.1642 18873 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20 Å2
2--0.18 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 2.42→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 148 41 3486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123558
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163345
X-RAY DIFFRACTIONr_angle_refined_deg2.7011.8384818
X-RAY DIFFRACTIONr_angle_other_deg0.8671.7937710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1515408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.7116.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19510634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.453.0991629
X-RAY DIFFRACTIONr_mcbond_other9.44718.8151629
X-RAY DIFFRACTIONr_mcangle_it13.5555.5632035
X-RAY DIFFRACTIONr_mcangle_other13.5655.8452036
X-RAY DIFFRACTIONr_scbond_it12.2963.3291929
X-RAY DIFFRACTIONr_scbond_other12.2981927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.726.0092783
X-RAY DIFFRACTIONr_long_range_B_refined19.3733920
X-RAY DIFFRACTIONr_long_range_B_other19.3793917
X-RAY DIFFRACTIONr_rigid_bond_restr7.933558
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.479 Å
RfactorNum. reflection% reflection
Rfree0.364 86 -
Rwork0.299 1366 -
obs--99.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6317-0.79991.75952.21370.19512.5183-0.02860.0437-0.23370.015-0.02060.05080.1966-0.03810.04920.0386-0.02080.0240.0196-0.00830.0326-15.8792-26.31010.152
24.2158-0.1765-0.32472.14820.41712.6410.0843-0.26910.3501-0.0754-0.04610.2637-0.2626-0.2071-0.03820.13560.0228-0.00920.0998-0.08660.1293-14.29314.547719.3762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 301
2X-RAY DIFFRACTION2B-3 - 302

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