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- PDB-9s1i: Crystal structure of human Dihydroorotate Dehydrogenase in comple... -

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Basic information

Entry
Database: PDB / ID: 9s1i
TitleCrystal structure of human Dihydroorotate Dehydrogenase in complex with arzanol
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / Pyrimidine Biosynthesis / Flavoprotein / DHODH / arzanol
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: 1.61 Å
AuthorsAlberti, M. / Miggiano, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaP2022P8KMF Italy
CitationJournal: J.Nat.Prod. / Year: 2025
Title: Arzanol Inhibits Human Dihydroorotate Dehydrogenase and Shows Antiviral Activity.
Authors: Alberti, M. / Tamburello, M. / Salamone, S. / Gallinella, G. / Sanna, C. / Appendino, G.B. / Lolli, M.L. / Massarotti, A. / Pollastro, F. / Miggiano, R.
History
DepositionJul 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 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)43,9027
Polymers42,6361
Non-polymers1,2666
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-18 kcal/mol
Surface area14100 Å2
Unit cell
Length a, b, c (Å)90.477, 90.477, 122.860
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


Mass: 42636.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The recombinant protein contains a polyhistidine tag at its N-terminal domain. Certain residues are absent in the solved structure as the corresponding electron density was of poor quality ...Details: The recombinant protein contains a polyhistidine tag at its N-terminal domain. Certain residues are absent in the solved structure as the corresponding electron density was of poor quality beacuse of high flexibility and conformational dynamics.
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02127

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Non-polymers , 6 types, 292 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-A1JKW / 3-[[3-ethanoyl-5-(3-methylbut-2-enyl)-2,4,6-tris(oxidanyl)phenyl]methyl]-6-ethyl-5-methyl-4-oxidanyl-pyran-2-one


Mass: 402.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.41 Å3/Da / Density % sol: 63.96 % / Description: Yellow cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2M Ammonium Sulphate, 100 mM Sodium Acetate pH 4.8, 20 % glycerol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 11, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.61→48.34 Å / Num. obs: 75934 / % possible obs: 100 % / Redundancy: 17.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.023 / Rrim(I) all: 0.096 / Net I/σ(I): 19.5
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 10956 / CC1/2: 0.939 / Rpim(I) all: 0.148 / Rrim(I) all: 0.624 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→48.34 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1755 3873 5.1 %
Rwork0.1639 --
obs0.1645 75879 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 85 286 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062847
X-RAY DIFFRACTIONf_angle_d0.8933867
X-RAY DIFFRACTIONf_dihedral_angle_d7.646417
X-RAY DIFFRACTIONf_chiral_restr0.058427
X-RAY DIFFRACTIONf_plane_restr0.011507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.25371130.21732571X-RAY DIFFRACTION100
1.63-1.650.2391480.19112529X-RAY DIFFRACTION100
1.65-1.670.20831500.1932531X-RAY DIFFRACTION100
1.67-1.690.1671310.18372525X-RAY DIFFRACTION100
1.69-1.720.26051230.18222542X-RAY DIFFRACTION100
1.72-1.740.19991330.17872581X-RAY DIFFRACTION100
1.74-1.770.22051380.17512542X-RAY DIFFRACTION100
1.77-1.80.18521680.17312507X-RAY DIFFRACTION100
1.8-1.830.20451310.1762573X-RAY DIFFRACTION100
1.83-1.860.20391380.18192542X-RAY DIFFRACTION100
1.86-1.90.19441320.18432541X-RAY DIFFRACTION100
1.9-1.940.19741400.16182548X-RAY DIFFRACTION100
1.94-1.980.18181580.16422556X-RAY DIFFRACTION100
1.98-2.030.14811150.15642557X-RAY DIFFRACTION100
2.03-2.080.15931440.15852548X-RAY DIFFRACTION100
2.08-2.130.17231550.15592523X-RAY DIFFRACTION100
2.13-2.20.15981470.15532571X-RAY DIFFRACTION100
2.2-2.270.16721200.15372590X-RAY DIFFRACTION100
2.27-2.350.17021160.162593X-RAY DIFFRACTION100
2.35-2.440.16941400.16382575X-RAY DIFFRACTION100
2.44-2.550.17411220.15892578X-RAY DIFFRACTION100
2.55-2.690.16551690.16012553X-RAY DIFFRACTION100
2.69-2.860.13721260.16112601X-RAY DIFFRACTION100
2.86-3.080.1561500.15132571X-RAY DIFFRACTION100
3.08-3.390.15871710.15692589X-RAY DIFFRACTION100
3.39-3.880.16831310.1482619X-RAY DIFFRACTION100
3.88-4.880.16591280.15082680X-RAY DIFFRACTION100
4.89-48.340.21411360.19562770X-RAY DIFFRACTION100

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