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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM DIHYDROOROTATE DEHYDROGENASE BOUND WITH INHIBITOR DSM421
 
Authors :  X. Deng, M. Phillips
Date :  12 Sep 16  (Deposition) - 28 Sep 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Alpha/Beta Barrel, Fmn, Mitochondrial Membrane, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Phillips, K. L. White, S. Kokkonda, X. Deng, J. White, F. El Mazouni, K. Marsh, D. R. Tomchick, K. Manjalanagara, K. R. Rudra G. Wirjanata, R. Noviyanti, R. N. Price, J. Marfurt, D. M. Shackleford F. C. Chiu, M. Campbell, M. B. Jimenez-Diaz, S. F. Bazaga, I. Angulo-Barturen, M. S. Martinez, M. Lafuente-Monasterio, W. Kaminsky, K. Silue, A. M. Zeeman, C. Kocken, D. Leroy, B. Blasco, E. Rossignol, T. Rueckle, D. Matthews, J. N. Burrows, D. Waterson, M. J. Palmer, P. K. Rathod, S. A. Charman
A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor With Improved Drug-Like Properties For Treatment And Prevention Of Malaria.
Acs Infect Dis V. 2 945 2016
PubMed-ID: 27641613  |  Reference-DOI: 10.1021/ACSINFECDIS.6B00144

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PET28B
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: PFF0160C
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Strain: ISOLATE 3D7
    Synonym: DHODEHASE,DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
178Z1Ligand/Ion2-(1,1-DIFLUOROETHYL)-5-METHYL-N-[6-(TRIFLUOROMETHYL)PYRIDIN-3-YL][1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
5ORO1Ligand/IonOROTIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:172 , LEU A:176 , GLY A:181 , GLU A:182 , CYS A:184 , HIS A:185 , PHE A:188 , LEU A:197 , PHE A:227 , LEU A:240 , ILE A:263 , ARG A:265 , ILE A:272 , LEU A:531 , VAL A:532 , MET A:536binding site for residue 78Z A 1001
2AC2SOFTWAREALA A:224 , ALA A:225 , GLY A:226 , LYS A:229 , THR A:249 , ASN A:274 , ASN A:342 , LYS A:429 , SER A:457 , ASN A:458 , SER A:477 , GLY A:478 , SER A:505 , GLY A:506 , GLY A:507 , TYR A:528 , SER A:529 , ORO A:1003 , HOH A:1106 , HOH A:1108 , HOH A:1119 , HOH A:1123binding site for residue FMN A 1002
3AC3SOFTWARELYS A:229 , ASN A:274 , CYS A:276 , GLY A:277 , PHE A:278 , ASN A:342 , ASN A:458 , THR A:459 , FMN A:1002binding site for residue ORO A 1003
4AC4SOFTWAREGLU A:164 , ASN A:195 , ILE A:196 , LEU A:197 , GOL A:1006binding site for residue LDA A 1004
5AC5SOFTWARELYS A:193 , GLY A:231 , VAL A:232 , ASN A:289 , LEU A:292 , PHE A:293 , ARG A:296binding site for residue GOL A 1005
6AC6SOFTWAREGLU A:164 , TYR A:199 , THR A:201 , LDA A:1004binding site for residue GOL A 1006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:248 -Thr A:249
2Lys A:260 -Pro A:261
3Ile A:456 -Ser A:457

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TBO)

(-) 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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhh.hhhhh..eeeeee.......hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh...hhhhh.........eeeeee....hhhhhhhhhhhhhhh...eeee.........hhhhh....eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tbo A 162 NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRK 565
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 ||    363       373       383|      423       433       443       453       463       473       483       493       503       513       523       533       543       553       563  
                                                                                                                                                                                                               343|                        383|                                                                                                                                                       
                                                                                                                                                                                                                356                         414
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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 5TBO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        PYRD_PLAF7 | Q08210: 1tv5 3i65 3i68 3i6r 3o8a 3sfk 4cq8 4cq9 4cqa 4orm 4rx0 5boo 5del 5fi8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5TBO)