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- PDB-9cze: High-Resolution Structure of Human DHODH for Molecular Replacemen... -

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Basic information

Entry
Database: PDB / ID: 9cze
TitleHigh-Resolution Structure of Human DHODH for Molecular Replacement in Fragment Screening Campaign
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / Crystallographic Fragment Screening / fragment-free protein / ligand identification.
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPurificacao, A.D. / Benz, L.S. / Froes, T.Q. / Weiss, M.S. / Nonato, M.C.
Funding support Brazil, European Union, 4items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)441038/2020-4 Brazil
Sao Paulo Research Foundation (FAPESP)2021/13237-5 Brazil
Sao Paulo Research Foundation (FAPESP)2020/06190-0 Brazil
iNEXT-Discovery871037European Union
CitationJournal: To Be Published
Title: Unexplored binding-sites on human DHODH identified by crystallographic fragment screening.
Authors: Purificacao, A.D. / Benz, L.S. / Froes, T.Q. / Weiss, M.S. / Nonato, M.C.
History
DepositionAug 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20413
Polymers39,9441
Non-polymers1,26112
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.597, 90.597, 123.232
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase / Dihydroorotate oxidase


Mass: 39943.613 Da / Num. of mol.: 1 / Fragment: residues 29-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 7 types, 293 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.87 Å3/Da / Density % sol: 68.19 % / Description: Square yellow crystals.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1 M sodium acetate trihydrate pH 4.8, 1.8 M ammonium sulfate and 30% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→48.46 Å / Num. obs: 77597 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 9.8 % / CC1/2: 0.971 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3816 / CC1/2: 0.595 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.41 / SU ML: 0.047 / Cross valid method: NONE / ESU R: 0.066 / ESU R Free: 0.066 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1968 3937 5.077 %
Rwork0.1802 73613 -
all0.181 --
obs-77550 99.915 %
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: 23.286 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20.003 Å20 Å2
2--0.006 Å2-0 Å2
3----0.019 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 80 281 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122898
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.6513952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.306526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25310467
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.65610115
X-RAY DIFFRACTIONr_chiral_restr0.0770.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022231
X-RAY DIFFRACTIONr_nbd_refined0.2070.21486
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2330
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.226
X-RAY DIFFRACTIONr_mcbond_it1.072.0931495
X-RAY DIFFRACTIONr_mcangle_it1.7373.7431890
X-RAY DIFFRACTIONr_scbond_it1.6622.2811403
X-RAY DIFFRACTIONr_scangle_it2.7154.1032057
X-RAY DIFFRACTIONr_lrange_it5.68725.4174772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3242630.2825413X-RAY DIFFRACTION99.9472
1.642-1.6860.2682770.2645276X-RAY DIFFRACTION100
1.686-1.7350.2452920.2475075X-RAY DIFFRACTION100
1.735-1.7890.2352940.224910X-RAY DIFFRACTION99.9808
1.789-1.8470.2062270.24895X-RAY DIFFRACTION100
1.847-1.9120.212360.194643X-RAY DIFFRACTION99.9795
1.912-1.9840.2122260.1854516X-RAY DIFFRACTION100
1.984-2.0650.1742620.1664318X-RAY DIFFRACTION100
2.065-2.1560.1912400.174146X-RAY DIFFRACTION99.9544
2.156-2.2620.1831900.174002X-RAY DIFFRACTION99.8809
2.262-2.3840.1672380.1623767X-RAY DIFFRACTION99.7758
2.384-2.5280.1731840.1613603X-RAY DIFFRACTION99.9472
2.528-2.7020.1861530.173394X-RAY DIFFRACTION99.7189
2.702-2.9180.1791820.1623166X-RAY DIFFRACTION100
2.918-3.1950.1791390.1572914X-RAY DIFFRACTION99.2523
3.195-3.570.1611390.1482657X-RAY DIFFRACTION100
3.57-4.1190.1671180.1542387X-RAY DIFFRACTION99.9202
4.119-5.0350.181210.1632001X-RAY DIFFRACTION99.8588
5.035-7.0830.266890.2241591X-RAY DIFFRACTION99.8811

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