Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH A LEFLUNOMIDE DERIVATIVE INHIBITOR 4
 
Authors :  M. Davis, T. Heikkila, G. A. Mcconkey, C. W. G. Fishwick, M. R. Parsons, A. P. Johnson
Date :  28 Jan 09  (Deposition) - 09 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrel, Tim-Barrel, Fad, Flavoprotein, Membrane, Mitochondrion, Mitochondrion Inner Membrane, Oxidoreductase, Polymorphism, Pyrimidine Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Davies, T. Heikkila, G. A. Mcconkey, C. W. G. Fishwick, M. R. Parsons, A. P. Johnson
Structure-Based Design, Synthesis, And Characterization Of Inhibitors Of Human And Plasmodium Falciparum Dihydroorotate Dehydrogenases
J. Med. Chem. V. 52 2683 2009
PubMed-ID: 19351152  |  Reference-DOI: 10.1021/JM800963T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
    ChainsA
    EC Number1.3.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 30-396
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDHODEHASE, DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MDY1Ligand/Ion(2Z)-N-(3-CHLORO-2'-METHOXYBIPHENYL-4-YL)-2-CYANO-3-HYDROXYBUT-2-ENAMIDE
3ORO1Ligand/IonOROTIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , ASN A:217 , ASN A:284 , THR A:285 , FMN A:398BINDING SITE FOR RESIDUE ORO A 1
2AC2SOFTWAREORO A:1 , ALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , ASN A:181 , ASN A:212 , LYS A:255 , THR A:283 , ASN A:284 , THR A:285 , SER A:305 , GLY A:306 , LEU A:309 , VAL A:333 , GLY A:334 , GLY A:335 , LEU A:355 , TYR A:356 , THR A:357 , HOH A:611 , HOH A:615BINDING SITE FOR RESIDUE FMN A 398
3AC3SOFTWARETYR A:38 , MET A:43 , PRO A:52 , HIS A:56 , ALA A:59 , THR A:63 , PHE A:98 , ARG A:136 , TYR A:356 , LEU A:359 , THR A:360 , PRO A:364 , HOH A:500BINDING SITE FOR RESIDUE MDY A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G0U)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:119 -Ser A:120
2Arg A:131 -Pro A:132
3Val A:282 -Thr A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_062413R135CPYRD_HUMANDisease (POADS)201230446AR136C
2UniProtVAR_062414G152RPYRD_HUMANDisease (POADS)267606766AG153R
3UniProtVAR_062415R199CPYRD_HUMANDisease (POADS)267606769AR200C
4UniProtVAR_062416G202APYRD_HUMANDisease (POADS)267606767AG203A
5UniProtVAR_062417G202DPYRD_HUMANDisease (POADS)267606767AG203D
6UniProtVAR_062418R244WPYRD_HUMANDisease (POADS)267606768AR245W
7UniProtVAR_062419T284IPYRD_HUMANDisease (POADS)  ---AT285I
8UniProtVAR_062420R346WPYRD_HUMANDisease (POADS)201947120AR347W
9UniProtVAR_062421D392GPYRD_HUMANDisease (POADS)779076692AD393G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHODEHASE_1PS00911 Dihydroorotate dehydrogenase signature 1.PYRD_HUMAN113-132  1A:114-133
2DHODEHASE_2PS00912 Dihydroorotate dehydrogenase signature 2.PYRD_HUMAN329-349  1A:330-350

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002192401ENSE00001420633chr16:72042643-7204268442PYRD_HUMAN1-770--
1.2ENST000002192402ENSE00000799143chr16:72045949-72046161213PYRD_HUMAN8-78711A:33-79 (gaps)47
1.3ENST000002192403ENSE00000692663chr16:72048372-72048571200PYRD_HUMAN79-145671A:80-14667
1.4ENST000002192404ENSE00000692662chr16:72050923-7205100583PYRD_HUMAN145-173291A:146-17429
1.5ENST000002192405ENSE00000692661chr16:72055023-72055210188PYRD_HUMAN173-235631A:174-23663
1.6ENST000002192406ENSE00000692660chr16:72056261-72056374114PYRD_HUMAN236-273381A:237-27438
1.7ENST000002192407ENSE00001718063chr16:72057064-72057217154PYRD_HUMAN274-325521A:275-32652
1.8ENST000002192408ENSE00001662402chr16:72057373-72057532160PYRD_HUMAN325-378541A:326-37954
1.9ENST000002192409ENSE00001737850chr16:72058044-72058954911PYRD_HUMAN378-395181A:379-39618

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:361
 aligned with PYRD_HUMAN | Q02127 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:364
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391    
           PYRD_HUMAN    32 GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 395
               SCOP domains d3g0ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3g0uA00 A:33-396 Aldolase class I                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---...hhhhheee..eee...eee.........hhhhhhhhh..eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------C----------------R----------------------------------------------C--A-----------------------------------------W---------------------------------------I-------------------------------------------------------------W---------------------------------------------G--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------DHODEHASE_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:33-79 (gaps) UniProt: 8-78    Exon 1.3  PDB: A:80-146 UniProt: 79-145                            ---------------------------Exon 1.5  PDB: A:174-236 UniProt: 173-235                      Exon 1.6  PDB: A:237-274              Exon 1.7  PDB: A:275-326 UniProt: 274-325           ----------------------------------------------------Exon 1.9           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:146-174     -------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:326-379 UniProt: 325-378             ----------------- Transcript 1 (2)
                 3g0u A  33 GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLP---FQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    42        52        62      |  -|       82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
                                                               69  73                                                                                                                                                                                                                                                                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G0U)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYRD_HUMAN | Q02127)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004152    dihydroorotate dehydrogenase activity    Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0048039    ubiquinone binding    Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0046134    pyrimidine nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0090140    regulation of mitochondrial fission    Any process that modulates the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0031000    response to caffeine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MDY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:131 - Pro A:132   [ RasMol ]  
    Gly A:119 - Ser A:120   [ RasMol ]  
    Val A:282 - Thr A:283   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3g0u
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.3.3.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  263750
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRD_HUMAN | Q021271d3g 1d3h 2b0m 2bxv 2fpt 2fpv 2fpy 2fqi 2prh 2prl 2prm 2wv8 3f1q 3fj6 3fjl 3g0x 3kvj 3kvk 3kvl 3kvm 3u2o 3w7r 3zws 3zwt 4igh 4jgd 4js3 4jts 4jtt 4jtu 4ls0 4ls1 4ls2 4oqv 4rk8 4rka 4rli 4rr4 4ylw 4zl1 4zmg 5h2z 5hin 5hqe 5k9c 5k9d 5mut 5mvc 5mvd

(-) Related Entries Specified in the PDB File

3f1q 3fj6 3fjl