[English] 日本語
Yorodumi
- PDB-1d3h: HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d3h
TitleHUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH ANTIPROLIFERATIVE AGENT A771726
ComponentsDIHYDROOROTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA BARREL / MEMBRANE BINDING MOTIF
Function / homology
Function and homology information


dihydroorotate dehydrogenase (quinone) / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase activity / Pyrimidine biosynthesis / response to L-arginine / regulation of mitochondrial fission / ubiquinone binding / response to caffeine / response to starvation / 'de novo' UMP biosynthetic process ...dihydroorotate dehydrogenase (quinone) / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase activity / Pyrimidine biosynthesis / response to L-arginine / regulation of mitochondrial fission / ubiquinone binding / response to caffeine / response to starvation / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / FMN binding / mitochondrial inner membrane / positive regulation of apoptotic process / neuronal cell body / response to xenobiotic stimulus => GO:0009410 / mitochondrion / integral component of membrane / nucleoplasm / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase / Dihydroorotate dehydrogenase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-A26 / ACETATE ION / OROTIC ACID / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 1.0Aug 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2012Group: Non-polymer description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8946
Polymers39,8571
Non-polymers1,0385
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

-
Components

-
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

-
Non-polymers , 6 types, 303 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-A26 / (2Z)-2-cyano-3-hydroxy-N-[4-(trifluoromethyl)phenyl]but-2-enamide / ANTIPROLIFERATIVE AGENT A771726 / Teriflunomide


Mass: 270.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F3N2O2 / Comment: medication*YM
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: ammonium sulphate, acetate buffer, glycerol, DDAO, C11DAO, A771726, 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 mMA7717261drop
120.1 Macetate1reservoir
132.4-2.6 Mammonium sulfate1reservoir
1430 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9134
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9134 Å / Relative weight: 1
ReflectionResolution: 1.8→23.5 Å / Num. all: 55112 / Num. obs: 54515 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.205 / Num. unique all: 7943 / % possible all: 100
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 264642 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.204

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
CNS0.5refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2713 5 %RANDOM
Rwork0.162 ---
obs0.162 53927 99 %-
all-55112 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.87 Å2 / ksol: 0.428 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.98 Å20 Å2
2--0.87 Å20 Å2
3----1.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 70 298 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d2.12
X-RAY DIFFRACTIONc_mcbond_it3.691.5
X-RAY DIFFRACTIONc_mcangle_it4.952
X-RAY DIFFRACTIONc_scbond_it5.482
X-RAY DIFFRACTIONc_scangle_it7.82.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 465 5.2 %
Rwork0.176 8495 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIGAND.PARLIGAND.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.12
X-RAY DIFFRACTIONc_mcbond_it3.691.5
X-RAY DIFFRACTIONc_scbond_it5.482
X-RAY DIFFRACTIONc_mcangle_it4.952
X-RAY DIFFRACTIONc_scangle_it7.82.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.207 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.176 / Rfactor obs: 0.176

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more