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- PDB-2b0m: Human dihydroorotate dehydrogenase bound to a novel inhibitor -

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Basic information

Entry
Database: PDB / ID: 2b0m
TitleHuman dihydroorotate dehydrogenase bound to a novel inhibitor
ComponentsDihydroorotate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / TIM barrel / alpha/beta barrel
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / 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) activity / dihydroorotate dehydrogenase (quinone) / 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-AMIDO-5-BIPHENYL-BENZOIC ACID / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHurt, D.E. / Sutton, A.E. / Clardy, J.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Brequinar derivatives and species-specific drug design for dihydroorotate dehydrogenase.
Authors: Hurt, D.E. / Sutton, A.E. / Clardy, J.
#1: Journal: To be Published
Title: Structure of Plasmodium falciparum dihyroorotate dehydrogenase with a bound inhibitor
Authors: Hurt, D.E. / Widom, J. / Clardy, J.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9404
Polymers43,0101
Non-polymers9303
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.398, 90.398, 123.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dihydroorotate dehydrogenase, mitochondrial / / E.C.1.3.3.1 / Dihydroorotate oxidase / DHOdehase


Mass: 43009.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Plasmid: pET-19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q02127, EC: 1.3.3.1
#2: Chemical ChemComp-201 / 3-AMIDO-5-BIPHENYL-BENZOIC ACID / 5-(AMINOCARBONYL)-1,1':4',1''-TERPHENYL-3-CARBOXYLIC ACID


Mass: 317.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15NO3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, C11DAO, C10DAO, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2000
RadiationMonochromator: Pair of vertically diffracting Si(111) crystals with the second crystal providing sagittal focusing, plus a Rhodium coated silicon mirror for vertical focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 39988 / Num. obs: 37871 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.109 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 8.4 / Rsym value: 0.37 / % possible all: 86.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D3G

1d3g


Resolution: 2→50 Å / Isotropic thermal model: Isotropic / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1866 -RANDOM
Rwork0.218 ---
all-37631 --
obs-35765 99.4 %-
Displacement parametersBiso mean: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.753 Å2-2.411 Å20 Å2
2---1.753 Å20 Å2
3---3.505 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 66 141 2964
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.2231.5
X-RAY DIFFRACTIONc_mcangle_it1.8152
X-RAY DIFFRACTIONc_scbond_it2.0562
X-RAY DIFFRACTIONc_scangle_it3.0342.5
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.29 156 -
Rwork0.25 --
obs-3241 85.8 %

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