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- PDB-9y7s: Crystal structure of Candida auris dihydrofolate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 9y7s
TitleCrystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1051 (R-form) and NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase Candida auris 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: 1.9 Å
AuthorsErlandsen, H. / Krucinska, J. / Wright, D.
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. / Krucinska, J. / Wright, D.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,4318
Polymers48,0952
Non-polymers2,3366
Water3,135174
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1994
Polymers24,0481
Non-polymers1,1513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2334
Polymers24,0481
Non-polymers1,1853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.018, 69.757, 112.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 180 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1CTA / 6-ethyl-5-[(3R)-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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 28% PEG3,350 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-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.9→32.97 Å / Num. obs: 36195 / % possible obs: 89.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.046 / Rrim(I) all: 0.123 / Χ2: 0.97 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→2 Å / % possible obs: 54.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 2.383 / Num. measured all: 20085 / Num. unique obs: 3189 / CC1/2: 0.293 / Rpim(I) all: 0.945 / Rrim(I) all: 2.578 / Χ2: 0.83 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→32.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.24 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 1694 4.8 %RANDOM
Rwork0.16271 ---
obs0.16586 33780 87.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0 Å2
2---0.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.9→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 157 174 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163372
X-RAY DIFFRACTIONr_angle_refined_deg2.5111.8384856
X-RAY DIFFRACTIONr_angle_other_deg0.8161.7917772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.9376.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93710639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
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_it7.8072.6231640
X-RAY DIFFRACTIONr_mcbond_other7.79914.4261640
X-RAY DIFFRACTIONr_mcangle_it10.0164.6952054
X-RAY DIFFRACTIONr_mcangle_other10.0264.9112055
X-RAY DIFFRACTIONr_scbond_it10.4522.8771944
X-RAY DIFFRACTIONr_scbond_other10.461941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.025.1652796
X-RAY DIFFRACTIONr_long_range_B_refined13.9374055
X-RAY DIFFRACTIONr_long_range_B_other13.9744029
X-RAY DIFFRACTIONr_rigid_bond_restr8.13533580
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.946 Å
RfactorNum. reflection% reflection
Rfree0.367 12 -
Rwork0.365 281 -
obs--10.02 %
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)
12.9460.67581.33691.8892-0.04352.1632-0.0222-0.0303-0.1783-0.0484-0.02860.0250.15190.01230.05080.06130.02450.03040.01130.01080.033-16.13948.6361-0.1199
23.60730.2215-0.25611.7644-0.1372.22150.04820.24360.24030.0359-0.0206-0.1967-0.13090.1736-0.02760.1235-0.0044-0.00310.07940.06970.0996-17.932539.4434-19.3935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 303
2X-RAY DIFFRACTION2B-3 - 303

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