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- PDB-9eg9: Crystal structure of human dihydroorotate dehydrogenase in comple... -

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Basic information

Entry
Database: PDB / ID: 9eg9
TitleCrystal structure of human dihydroorotate dehydrogenase in complex with lapachol
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / quinone / lapachol
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
: / ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsPurificacao, A.D. / Benz, L.S. / Weiss, M.S. / Nonato, M.C.
Funding support Brazil, European Union, Germany, 5items
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
German Research Foundation (DFG)FE2166/1-1 Germany
CitationJournal: Acs Omega / Year: 2025
Title: Crystallographic Structure of Human Dihydroorotate Dehydrogenase in Complex with the Natural Product Inhibitor Lapachol.
Authors: Purificacao, A.D. / Benz, L.S. / Lima Silva, W.J. / Emery, F.S. / Andrade, C.H. / Weiss, M.S. / Nonato, M.C.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 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)41,42211
Polymers39,9441
Non-polymers1,47810
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.460, 90.460, 122.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 7 types, 255 molecules

#2: 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
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-A1BIJ / 2-hydroxy-3-(3-methylbut-2-en-1-yl)naphthalene-1,4-dione


Mass: 242.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.63 Å3/Da / Density % sol: 66.09 % / Description: Yellow square 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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.31→48.34 Å / Num. obs: 139283 / % possible obs: 100 % / Redundancy: 19.96 % / Biso Wilson estimate: 22.57 Å2 / CC1/2: 1 / Net I/σ(I): 18.45
Reflection shellResolution: 1.31→1.39 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 22325 / CC1/2: 0.412 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
pointless1.12.10data scaling
XDSdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→48.34 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.838 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17997 6855 4.9 %RANDOM
Rwork0.17398 ---
obs0.17427 132428 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.329 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.31→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 97 245 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172854
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6674119
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5896600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97620.676148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87615488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2041527
X-RAY DIFFRACTIONr_chiral_restr0.0710.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it1.1842.0131520
X-RAY DIFFRACTIONr_mcbond_other1.1832.0111517
X-RAY DIFFRACTIONr_mcangle_it1.893.0171910
X-RAY DIFFRACTIONr_mcangle_other1.893.0181911
X-RAY DIFFRACTIONr_scbond_it1.8422.2491498
X-RAY DIFFRACTIONr_scbond_other1.8412.2511499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7843.2822195
X-RAY DIFFRACTIONr_long_range_B_refined4.72724.5453514
X-RAY DIFFRACTIONr_long_range_B_other4.49724.0273451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 469 -
Rwork0.33 9703 -
obs--99.89 %

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