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- PDB-1d3g: HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG -

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Basic information

Entry
Database: PDB / ID: 1d3g
TitleHUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG
ComponentsDIHYDROOROTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PROTEIN-ANTIPROLIFERATIVE AGENT COMPLEX
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
ACETATE ION / Chem-BRE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsLiu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents.
Authors: Liu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J.
History
DepositionSep 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1837
Polymers39,8571
Non-polymers1,3266
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.610, 90.610, 122.410
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 /


Mass: 39856.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02127, EC: 1.3.3.1

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Non-polymers , 7 types, 280 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BRE / 2-BIPHENYL-4-YL-6-FLUORO-3-METHYL-QUINOLINE-4-CARBOXYLIC ACID / BREQUINAR ANALOG


Mass: 357.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16FNO2
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#7: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: AMMONIUM SULFATE, ACETATE, GLYCEROL, DDAO, C11DAO, BREQUINAR, OROTATE, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mM1dropC11DAO
3200 mM1dropNaCl
415 %glycerol1drop
50.5 mMEDTA1drop
625 mMHEPES1drop
70.05 Macetate1drop
810.4 mMDDAO1drop
91 mMDHO1drop
101.2-1.3 Mammonium sulfate1drop
110.5 mMBrequinar1drop
120.1 Macetate1reservoir
132.4-2.6 Mammonium sulfate1reservoir
1430 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.936
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 77790 / Num. obs: 75457 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / % possible all: 83.5
Reflection
*PLUS
% possible obs: 97.1 % / Num. measured all: 444987
Reflection shell
*PLUS
% possible obs: 84.8 %

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.6→30 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3781 5 %RANDOM
Rwork0.168 ---
all-77811 --
obs-75301 97 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.53 Å20 Å2
2--1.66 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 92 274 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.23
X-RAY DIFFRACTIONp_mcangle_it2.874
X-RAY DIFFRACTIONp_scbond_it3.23
X-RAY DIFFRACTIONp_scangle_it4.424
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.194 514 4.7 %
Rwork0.166 10314 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIGAND.PARLIGAND.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: REFMAC / Version: 4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_deg2
X-RAY DIFFRACTIONp_mcbond_it2.23
X-RAY DIFFRACTIONp_scbond_it3.23
X-RAY DIFFRACTIONp_mcangle_it2.874
X-RAY DIFFRACTIONp_scangle_it4.424
LS refinement shell
*PLUS
Rfactor obs: 0.166

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