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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM DIHYDROOROTATE DEHYDROGENASE BOUNDED WITH DSM422 (TETRAHYDRO-2-NAPHTHYL AND 2-INDANYL TRIAZOLOPYRIMIDINE)
 
Authors :  X. Deng, S. Kokkonda, D. Tomchick, M. Phillips
Date :  22 Dec 15  (Deposition) - 18 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Fmn, Alpha/Beta Barrel, Inhibitor, Oxidoreductase / Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kokkonda, X. Deng, K. L. White, J. M. Coteron, M. Marco, L. De Las Heras, J. White, F. El Mazouni, D. R. Tomchick, K. Manjalanagara, K. R. Rudra, G. Chen, J. Morizzi, E. Ryan, W. Kaminsky, D. Leroy, M. S. Martinez-Martinez, M. B. Jimenez-Diaz, S. F. Bazaga, I. Angulo-Barturen, D. Waterson, J. N. Burrows, D. Matthews, S. A. Charman, M. A. Phillips, P. K. Rathod
Tetrahydro-2-Naphthyl And 2-Indanyl Triazolopyrimidines Targeting Plasmodium Falciparum Dihydroorotate Dehydrogenas Display Potent And Selective Antimalarial Activity.
J. Med. Chem. V. 59 5416 2016
PubMed-ID: 27127993  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00275

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 158-569
    Gene: PFF0160C
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Other Details: DELETION OF LOOP (384-413)
    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  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
15Y51Ligand/Ion2-[1,1-BIS(FLUORANYL)ETHYL]-~{N}-[(2~{S})-7-BROMANYL-1,2,3,4-TETRAHYDRONAPHTHALEN-2-YL]-5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
4ORO1Ligand/IonOROTIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:172 , CYS A:175 , GLY A:181 , GLU A:182 , CYS A:184 , HIS A:185 , PHE A:188 , LEU A:197 , PHE A:227 , CYS A:233 , ILE A:237 , ILE A:263 , ARG A:265 , ILE A:272 , LEU A:531 , VAL A:532 , MET A:536binding site for residue 5Y5 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:1102 , HOH A:1104 , HOH A:1120binding site for residue FMN A 1002
3AC3SOFTWAREASN 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 , TYR A:199binding site for residue LDA A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FI8)

(-) 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 5FI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FI8)

(-) Exons   (0, 0)

(no "Exon" information available for 5FI8)

(-) 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:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhh...hhhhh.........eeeeee....hhhhhhhhhhhhhhh...eeee.........hhhhh....eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fi8 A 162 NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRK 565
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 ||    362       372       382||     422       432       442       452       462       472       482       492       502       512       522       532       542       552       562   
                                                                                                                                                                                                               343|                         383|                                                                                                                                                       
                                                                                                                                                                                                                355                          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 5FI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FI8)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 5tbo

(-) Related Entries Specified in the PDB File

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