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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE (DHODH) WITH NO.33 COMPOUND
 
Authors :  D. Wu, P. Ouyang, W. Lu, J. Huang
Date :  06 Mar 15  (Deposition) - 09 Mar 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Rheumatoid Arthritis, Complex, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Wu, P. Ouyang, W. Lu, J. Huang
Crystal Structure Of Human Dihydroorotate Dehydrogenase (Dhodh) With No. 33 Compound
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 BL21
    Expression System Plasmid: PET19B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    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/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
152Y1Ligand/IonMETHYL (2Z)-CYANO[3-(3-FLUORO-4'-METHOXYBIPHENYL-4-YL)-4-OXO-1,3-THIAZOLIDIN-2-YLIDENE]ACETATE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3ORO1Ligand/IonOROTIC ACID
4SO410Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:38 , LEU A:46 , LEU A:58 , ALA A:59 , PHE A:62 , THR A:63 , LEU A:67 , LEU A:68 , PRO A:69 , ILE A:94 , PHE A:98 , LEU A:359 , PRO A:364 , HOH A:598binding site for residue 52Y A 401
02AC2SOFTWAREALA 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:403 , HOH A:517 , HOH A:525binding site for residue FMN A 402
03AC3SOFTWARELYS 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:402binding site for residue ORO A 403
04AC4SOFTWAREARG A:160 , GLN A:325binding site for residue SO4 A 404
05AC5SOFTWAREARG A:245 , HIS A:248 , HOH A:505binding site for residue SO4 A 405
06AC6SOFTWAREGLN A:168 , ALA A:169 , THR A:172 , LEU A:205 , ASP A:207 , HOH A:501 , HOH A:555 , HOH A:576binding site for residue SO4 A 406
07AC7SOFTWARETHR A:261 , SER A:262 , HOH A:503binding site for residue SO4 A 407
08AC8SOFTWARELYS A:170 , THR A:261 , GLN A:263 , HOH A:503binding site for residue SO4 A 408
09AC9SOFTWAREARG A:245 , ARG A:246 , ARG A:249 , THR A:301 , SO4 A:413 , HOH A:518binding site for residue SO4 A 409
10AD1SOFTWAREALA A:219 , GLY A:220 , ARG A:222 , HOH A:594binding site for residue SO4 A 410
11AD2SOFTWAREALA A:71 , ARG A:72 , PHE A:73 , HOH A:539 , HOH A:601binding site for residue SO4 A 411
12AD3SOFTWARELYS A:307 , PRO A:308 , ASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , HOH A:559binding site for residue SO4 A 412
13AD4SOFTWAREARG A:246 , ARG A:249 , SO4 A:409binding site for residue SO4 A 413

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:70 -Ala A:71
2Gly A:119 -Ser A:120
3Arg A:131 -Pro A:132
4Val A:282 -Thr A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YLW)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ylw A  33 GDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    42        52        62        72        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 4YLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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    Arg A:131 - Pro A:132   [ RasMol ]  
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  PYRD_HUMAN | Q02127
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  1.3.5.2
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 Related Entries

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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 4jtu 4ls0 4ls1 4ls2 4oqv 4rk8 4rka 4rli 4rr4 4zl1 4zmg 5h2z 5hin 5hqe 5k9c 5k9d 5mut 5mvc 5mvd

(-) Related Entries Specified in the PDB File

4ls0