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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE AT 1.7 A RESOLUTION
 
Authors :  T. A. Lewis, D. B. Sykes, J. M. Law, B. Munoz, D. T. Scadden, J. K. Rustigue M. C. Nonato, S. L. Schreiber
Date :  31 May 16  (Deposition) - 12 Oct 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Alpha/Beta Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Lewis, D. B. Sykes, J. M. Law, B. Munoz, J. K. Rustiguel, M. C. Nonato, D. T. Scadden, S. L. Schreiber
Development Of Ml390: A Human Dhodh Inhibitor That Induces Differentiation In Acute Myeloid Leukemia.
Acs Med Chem Lett V. 7 1112 2016
PubMed-ID: 27994748  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00316

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 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  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CE91Ligand/IonDODECYL NONA ETHYLENE GLYCOL ETHER
3CL3Ligand/IonCHLORIDE ION
4FNR1Ligand/Ion1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
5GOL1Ligand/IonGLYCEROL
6ORO1Ligand/IonOROTIC ACID
7SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA 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:401 , HOH A:551 , HOH A:576binding site for residue FNR A 400
02AC2SOFTWARELYS 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 , FNR A:400binding site for residue ORO A 401
03AC3SOFTWAREMET A:43 , LEU A:46 , ALA A:55 , HIS A:56 , ALA A:59 , THR A:63 , THR A:360 , HOH A:731binding site for residue CE9 A 402
04AC4SOFTWAREARG A:245 , VAL A:247 , HIS A:248 , HOH A:515binding site for residue SO4 A 403
05AC5SOFTWAREARG A:249 , HOH A:680binding site for residue SO4 A 404
06AC6SOFTWAREGLN A:168 , ALA A:169 , THR A:172 , LEU A:205 , ALA A:206 , ASP A:207 , HOH A:513 , HOH A:630 , HOH A:692binding site for residue ACT A 405
07AC7SOFTWAREARG A:160 , HOH A:739binding site for residue ACT A 406
08AC8SOFTWAREASP A:311 , THR A:314 , GLN A:315 , ARG A:318 , GLU A:344 , HOH A:543binding site for residue ACT A 407
09AC9SOFTWAREGLN A:165 , PRO A:204 , HIS A:248 , ARG A:298 , SER A:299binding site for residue CL A 408
10AD1SOFTWAREARG A:347 , GLN A:381 , HOH A:535 , HOH A:558binding site for residue CL A 409
11AD2SOFTWAREARG A:245 , THR A:301 , GLY A:302 , HOH A:676 , HOH A:804binding site for residue CL A 410
12AD3SOFTWARESER A:155 , HOH A:651 , HOH A:837binding site for residue GOL A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K9D)

(-) 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  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K9D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K9D)

(-) Exons   (0, 0)

(no "Exon" information available for 5K9D)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k9d A  38 YAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR 396
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
   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  (0, 0)

(no "SCOP Domain" information available for 5K9D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K9D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K9D)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:131 - Pro A:132   [ RasMol ]  
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    Val A:282 - Thr A:283   [ RasMol ]  
 

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  1.3.5.2
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 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 4jtu 4ls0 4ls1 4ls2 4oqv 4rk8 4rka 4rli 4rr4 4ylw 4zl1 4zmg 5h2z 5hin 5hqe 5k9c 5mut 5mvc 5mvd

(-) Related Entries Specified in the PDB File

5k9c 5K9C CONTAINS THE SAME PROTEIN COMPLEXED WITH INHIBITOR