Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE (DHODH) WITH BREQUINAR ANALOGUE
 
Authors :  L. Zhu, J. Zhu, X. Ren, H. Li
Date :  24 Mar 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Fmn Binding, Mitochondria Inner Membrane, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zhu, H. Li, J. Zhu, X. Ren
Crystal Structure Of Human Dihydroorotate Dehydrogenase (Dhodh) With 057
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-395
    Gene: DHODH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DHODEHASE, DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1DET1Ligand/IonUNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3JTU1Ligand/Ion6-BROMO-2-{4-[(2R)-BUTAN-2-YL]PHENYL}-3-METHYLQUINOLINE-4-CARBOXYLIC ACID
4ORO1Ligand/IonOROTIC ACID
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
1DET2Ligand/IonUNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3JTU2Ligand/Ion6-BROMO-2-{4-[(2R)-BUTAN-2-YL]PHENYL}-3-METHYLQUINOLINE-4-CARBOXYLIC ACID
4ORO2Ligand/IonOROTIC ACID
5SO46Ligand/IonSULFATE ION
Biological Unit 2 (5, 7)
No.NameCountTypeFull Name
1DET1Ligand/IonUNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3JTU1Ligand/Ion6-BROMO-2-{4-[(2R)-BUTAN-2-YL]PHENYL}-3-METHYLQUINOLINE-4-CARBOXYLIC ACID
4ORO1Ligand/IonOROTIC ACID
5SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , TYR A:147 , 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 , ORO A:402 , HOH A:501 , HOH A:510BINDING SITE FOR RESIDUE FMN A 401
2AC2SOFTWARELYS 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:401BINDING SITE FOR RESIDUE ORO A 402
3AC3SOFTWAREARG A:245 , VAL A:247 , HIS A:248BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREARG A:160BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:524BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWAREARG A:57 , GLN A:126 , GLU A:127 , SER A:151 , HIS A:152BINDING SITE FOR RESIDUE DET A 406
7AC7SOFTWAREMET A:43 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , THR A:63 , LEU A:68 , VAL A:134 , ARG A:136 , TYR A:356 , THR A:360 , HOH A:614BINDING SITE FOR RESIDUE JTU A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JTU)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric 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  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JTU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JTU)

(-) Exons   (0, 0)

(no "Exon" information available for 4JTU)

(-) Sequences/Alignments

Asymmetric 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4jtua_ A: Dihydroorotate dehydrogenase                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jtu A  32 TGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    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
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JTU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JTU)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    DET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JTU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ 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 ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4jtu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.3.5.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYRD_HUMAN | Q02127
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PYRD_HUMAN | Q02127: 1d3g 1d3h 2b0m 2bxv 2fpt 2fpv 2fpy 2fqi 2prh 2prl 2prm 2wv8 3f1q 3fj6 3fjl 3g0u 3g0x 3kvj 3kvk 3kvl 3kvm 3u2o 3w7r 3zws 3zwt 4igh 4jgd 4js3 4jts 4jtt 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

4js3 4jts 4jtt