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- PDB-9y7u: Crystal structure of Candida auris dihydrofolate reductase in com... -

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Basic information

Entry
Database: PDB / ID: 9y7u
TitleCrystal structure of Candida auris dihydrofolate reductase in complex with inhibitor 1282 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: 1.65 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)49,89610
Polymers47,2682
Non-polymers2,6288
Water4,125229
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9485
Polymers23,6341
Non-polymers1,3144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9485
Polymers23,6341
Non-polymers1,3144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.323, 73.567, 93.376
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 202 / Label seq-ID: 4 - 203

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase


Mass: 23634.137 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, 237 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-A1CS9 / 4-{7-[(2S)-4-(2,4-diaminopyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-5-yl}-2,6-difluorophenol


Mass: 410.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16F2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 277 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-2 / Wavelength: 0.97931 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: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.65→34.22 Å / Num. obs: 50319 / % possible obs: 94.7 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.032 / Rrim(I) all: 0.045 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.681.90.6911.125010.5380.6910.97796.4
9.04-34.221.60.00831.637610.0080.01197.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PHASERphasing
AutoProcessdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→34.22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.402 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 2614 5.2 %RANDOM
Rwork0.1513 47659 --
all0.155 ---
obs-50273 94.498 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.293 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0 Å2
2---0.999 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 174 229 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163322
X-RAY DIFFRACTIONr_angle_refined_deg2.3181.8384816
X-RAY DIFFRACTIONr_angle_other_deg0.7961.7917660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.5756.66736
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg5.051512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12210628
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.17910160
X-RAY DIFFRACTIONr_chiral_restr0.1190.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2110.2617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.23153
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2186
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.28
X-RAY DIFFRACTIONr_nbd_other0.170.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.212
X-RAY DIFFRACTIONr_mcbond_it5.3951.631612
X-RAY DIFFRACTIONr_mcbond_other5.3751.631612
X-RAY DIFFRACTIONr_mcangle_it7.4622.9242016
X-RAY DIFFRACTIONr_mcangle_other7.4652.9242017
X-RAY DIFFRACTIONr_scbond_it7.2831.9541938
X-RAY DIFFRACTIONr_scbond_other7.061.9431931
X-RAY DIFFRACTIONr_scangle_it10.2123.4462798
X-RAY DIFFRACTIONr_scangle_other9.8893.422787
X-RAY DIFFRACTIONr_lrange_it13.24417.9513992
X-RAY DIFFRACTIONr_lrange_other13.02317.4833946
X-RAY DIFFRACTIONr_rigid_bond_restr5.66836872
X-RAY DIFFRACTIONr_ncsr_local_group_10.1260.056345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.12640.05008
12AX-RAY DIFFRACTIONLocal ncs0.12640.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.3231980.2863535X-RAY DIFFRACTION96.5847
1.693-1.7390.3011970.2753464X-RAY DIFFRACTION96.6473
1.739-1.7890.2921880.2333380X-RAY DIFFRACTION96.9829
1.789-1.8440.2611820.1933297X-RAY DIFFRACTION97.2331
1.844-1.9050.2461850.1713097X-RAY DIFFRACTION94.6094
1.905-1.9710.2481150.1542065X-RAY DIFFRACTION65.3673
1.971-2.0450.2361900.1433007X-RAY DIFFRACTION97.6481
2.045-2.1290.2311400.1342921X-RAY DIFFRACTION98.2034
2.129-2.2230.2051490.1162796X-RAY DIFFRACTION98.2977
2.223-2.3310.2091060.1292066X-RAY DIFFRACTION75.6004
2.331-2.4560.2461480.1372555X-RAY DIFFRACTION98.2552
2.456-2.6040.2421320.1422436X-RAY DIFFRACTION98.9214
2.604-2.7830.2471170.152277X-RAY DIFFRACTION98.2355
2.783-3.0040.2361130.1532161X-RAY DIFFRACTION98.7837
3.004-3.2890.2531010.1582004X-RAY DIFFRACTION99.1055
3.289-3.6730.193850.1461814X-RAY DIFFRACTION99.0094
3.673-4.2330.23870.1291631X-RAY DIFFRACTION99.0773
4.233-5.1640.16750.1151382X-RAY DIFFRACTION99.4539
5.164-7.2220.186670.1571097X-RAY DIFFRACTION99.4872
7.222-34.220.213390.171674X-RAY DIFFRACTION98.8904
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)
12.3394-0.0346-0.75211.24960.0691.31390.00540.10560.1606-0.05620.0051-0.0542-0.0559-0.0135-0.01050.04050.009-0.01050.0080.00470.018415.326-9.9139-3.1907
23.05810.54640.20192.16890.17111.82190.01850.1476-0.1597-0.0583-0.03310.1657-0.0067-0.09910.01450.06670.00810.0060.0347-0.04640.086916.3323-44.3962-12.8291
Refinement TLS groupSelection: ALL

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