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- PDB-9y7r: Crystal structure of Candida auris dihydrofolate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 9y7r
TitleCrystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1283 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: 2.13 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
B: Dihydrofolate reductase
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4356
Polymers48,0952
Non-polymers2,3404
Water1,09961
1
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2173
Polymers24,0481
Non-polymers1,1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2173
Polymers24,0481
Non-polymers1,1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.623, 72.224, 105.442
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-A1CTB / 4-{7-[(2R)-4-(2,4-diamino-6-methylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-5-yl}-2,6-difluorophenol


Mass: 424.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18F2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG 3,350 0.2M LiSO4 0.1M Pipes, pH 6.5

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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: 0.92091 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: 0.92091 Å / Relative weight: 1
ReflectionResolution: 2.13→32.33 Å / Num. obs: 28377 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.051 / Net I/σ(I): 9.7
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2293 / CC1/2: 0.408 / Rrim(I) all: 0.807 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→32.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.943 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1473 5.2 %RANDOM
Rwork0.18172 ---
obs0.18454 26903 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.738 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å2-0 Å2
2--0.44 Å2-0 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.13→32.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 158 61 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163332
X-RAY DIFFRACTIONr_angle_refined_deg2.5111.8424818
X-RAY DIFFRACTIONr_angle_other_deg0.8661.7947682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.2876.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00810634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
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_it3.5582.7281618
X-RAY DIFFRACTIONr_mcbond_other3.562.7281618
X-RAY DIFFRACTIONr_mcangle_it4.8024.8812026
X-RAY DIFFRACTIONr_mcangle_other4.8014.8822027
X-RAY DIFFRACTIONr_scbond_it5.263.2321932
X-RAY DIFFRACTIONr_scbond_other5.2593.2321933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5335.6892793
X-RAY DIFFRACTIONr_long_range_B_refined9.10927.173989
X-RAY DIFFRACTIONr_long_range_B_other9.11227.173988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.183 Å
RfactorNum. reflection% reflection
Rfree0.324 97 -
Rwork0.312 1953 -
obs--99.95 %
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)
13.5206-0.41581.54711.98130.20392.29130.0004-0.0663-0.2743-0.00710.0034-0.02610.1925-0.0055-0.00380.055-0.01330.02540.01050.00250.0366-16.9081-26.7740.9442
23.89860.4590.10462.48870.63132.39830.0333-0.24370.2181-0.0804-0.05220.184-0.2054-0.23110.0190.1920.0433-0.03580.0874-0.08530.1277-14.67125.595417.5441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 302
2X-RAY DIFFRACTION2A3 - 302

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