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- PDB-3f1q: Human dihydroorotate dehydrogenase in complex with a leflunomide ... -

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Basic information

Entry
Database: PDB / ID: 3f1q
TitleHuman dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 1
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / Dihydroorotate dehydrogenase / leflunomide / FAD / Flavoprotein / Membrane / Mitochondrion / Mitochondrion inner membrane / Pyrimidine biosynthesis / Transit peptide
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
ACETIC ACID / Chem-BCE / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHeikkila, T. / Davies, M. / McConkey, G.A. / Fishwick, C.W.G. / Parsons, M.R. / Johnson, A.P.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases
Authors: Davies, M. / Heikkila, T. / McConkey, G.A. / Fishwick, C.W.G. / Parsons, M.R. / Johnson, A.P.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_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

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9637
Polymers39,8571
Non-polymers1,1076
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.696, 90.696, 122.950
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 / / DHOdehase / Dihydroorotate oxidase


Mass: 39856.535 Da / Num. of mol.: 1 / Fragment: residues 30-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli) / References: UniProt: Q02127, EC: 1.3.3.1

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Non-polymers , 6 types, 317 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-BCE / (2Z)-N-biphenyl-4-yl-2-cyano-3-hydroxybut-2-enamide


Mass: 278.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: drops: 50mM HEPES, pH 7.7, 400mM NaCl, 30% glycerol, 1mM EDTA, 10mM N,N-dimethylundecylamin-N-oxide (C11DAO), precipitant solution: 0.1M acetate pH 4.6-5.0, 40mM C11DAO, 20.8mM N,N- ...Details: drops: 50mM HEPES, pH 7.7, 400mM NaCl, 30% glycerol, 1mM EDTA, 10mM N,N-dimethylundecylamin-N-oxide (C11DAO), precipitant solution: 0.1M acetate pH 4.6-5.0, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM dihydroorotate (DHO), 1.8-2.4M ammonium sulfate, 1mM inhibitors, reservoir: 0.1M acetate pH 4.8, 2.4-2.6M ammonium sulfate, 30% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30.74 Å / Num. all: 40134 / Num. obs: 40134 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 6.1 / Num. unique all: 5807 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D3H

1d3h


Resolution: 2→29.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.541 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19937 2011 5 %RANDOM
Rwork0.17839 ---
obs0.17947 36072 99.96 %-
all-38083 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 76 311 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222900
X-RAY DIFFRACTIONr_angle_refined_deg1.0852.0133924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62323.04125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6471530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022194
X-RAY DIFFRACTIONr_nbd_refined0.1960.21478
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.225
X-RAY DIFFRACTIONr_mcbond_it0.2571.51855
X-RAY DIFFRACTIONr_mcangle_it0.39422877
X-RAY DIFFRACTIONr_scbond_it1.08131206
X-RAY DIFFRACTIONr_scangle_it1.8234.51046
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 124 -
Rwork0.184 2794 -
obs-2794 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
131.872519.6771-39.4815142.2053-17.761349.24330.8146-2.4492.4067.31441.1683-3.3538-3.50153.3983-1.98290.27380.00030.02230.24510.01040.2627.5514-20.8028-4.9817
24.6783-4.0832-4.158939.34029.26095.09590.00060.80040.2544-1.55650.38020.02380.0403-0.1598-0.38080.0137-0.0260.05670.15090.101-0.06616.047-29.8443-10.1899
35.14876.56476.78388.41829.133913.8236-0.08610.5902-0.4232-0.18040.4329-0.5940.15311.2624-0.3468-0.04110.05230.03590.176800.009610.1304-39.8754-1.5381
44.2385-2.2302-0.54093.50450.99470.7764-0.044-0.1320.4642-0.0090.0848-0.5105-0.42060.1568-0.04090.0179-0.0762-0.06220.0019-0.04120.08152.3162-23.320515.498
50.9735-0.22270.82550.4786-0.20790.90630.08390.0927-0.0527-0.0435-0.0588-0.04740.05250.1825-0.0251-0.02250.01330.00790.03930.00420.0024.0995-41.9847.3763
61.0686-0.40810.10080.3138-0.3811.0433-0.0194-0.1042-0.06170.0104-0.0260.00030.1213-0.01880.0455-0.0050.0085-0.00780.02970.0199-0.00410.7798-44.571518.4403
73.1586-0.1221.83120.2414-0.04562.0751-0.0863-0.252-0.17420.03270.08750.0308-0.018-0.1927-0.0012-0.01260.00680.01810.03760.02060.0129-10.3736-44.915323.4458
80.6875-0.1938-0.07430.50050.5531.49150.0206-0.0407-0.035-0.04060.00070.04840.0713-0.0689-0.0213-0.01920.0108-0.0117-0.0034-0.0003-0.0019-13.3676-39.54464.4097
91.2612-0.10930.06680.9353-0.01880.9686-0.0552-0.03790.13680.01020.0179-0.0502-0.1488-0.01170.0373-0.00710.0097-0.0318-0.0011-0.00990.0008-9.2177-25.76769.6419
1019.3386-4.3793-4.032419.805310.954431.7677-0.0602-0.65851.2409-0.24490.54360.6652-1.1079-0.7528-0.4834-0.04410.03910.0040.0754-0.04950.0574-22.9126-22.755915.2991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 36
2X-RAY DIFFRACTION2A37 - 49
3X-RAY DIFFRACTION3A50 - 64
4X-RAY DIFFRACTION4A65 - 89
5X-RAY DIFFRACTION5A90 - 163
6X-RAY DIFFRACTION6A164 - 225
7X-RAY DIFFRACTION7A226 - 273
8X-RAY DIFFRACTION8A274 - 319
9X-RAY DIFFRACTION9A320 - 392
10X-RAY DIFFRACTION10A393 - 396

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