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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR IN COMPLEX WITH 4-NITROPHENYL ISOTHIOCYANATE
 
Authors :  M. P. Pinheiro, F. S. Emery, M. C. Nonato
Date :  29 Mar 12  (Deposition) - 12 Dec 12  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Leishmania Major, Dihydroorotate Dehydrogenase, 4-Nitrophenyl Isothiocyanate, Pyrd, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. P. Pinheiro, F. S. Emery, M. C. Nonato
Target Sites For The Design Of Anti-Trypanosomatid Drugs Based On The Structure Of Dihydroorotate Dehydrogenase.
Curr. Pharm. Des. V. 19 2615 2013
PubMed-ID: 23116399

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DHODH, LMJF16.0530, LMJF_16_0530
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: FRIEDLIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
14NF2Ligand/IonN-(4-NITROPHENYL)THIOFORMAMIDE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4SO47Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:101 , LEU A:102 , SER A:103 , MET A:104 , ASN A:107 , VAL A:140 , CYS A:150 , HOH A:732BINDING SITE FOR RESIDUE 4NF A 401
02AC2SOFTWAREALA A:19 , ALA A:20 , GLY A:21 , LYS A:44 , SER A:45 , ASN A:68 , MET A:70 , ASN A:128 , LYS A:165 , ILE A:194 , ASN A:195 , GLY A:222 , GLY A:223 , VAL A:226 , CYS A:249 , GLY A:250 , GLY A:251 , GLY A:272 , THR A:273 , SO4 A:403 , HOH A:504 , HOH A:516 , HOH A:517 , HOH A:525BINDING SITE FOR RESIDUE FMN A 402
03AC3SOFTWARELYS A:44 , ASN A:68 , MET A:70 , GLY A:71 , LEU A:72 , PRO A:73 , CYS A:131 , ASN A:133 , FMN A:402 , HOH A:501BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREHIS A:160 , SER A:161 , HOH A:643BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREILE A:203 , SO4 A:408 , HOH A:562 , HOH A:568 , LEU B:231BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARETHR A:25 , ARG A:51 , PRO A:73 , ASN A:74 , ASN A:75 , HOH A:593 , HOH A:632BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWARETYR A:59 , HOH A:574BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREVAL A:202 , ILE A:203 , ASP A:204 , ARG A:298 , GOL A:405 , HOH A:764BINDING SITE FOR RESIDUE SO4 A 408
09AC9SOFTWAREGLY B:101 , LEU B:102 , SER B:103 , MET B:104 , ASN B:107 , LYS B:137 , PRO B:138 , VAL B:140 , CYS B:150 , HOH B:631BINDING SITE FOR RESIDUE 4NF B 401
10BC1SOFTWAREALA B:19 , ALA B:20 , GLY B:21 , LYS B:44 , SER B:45 , ASN B:68 , MET B:70 , ASN B:128 , LYS B:165 , ILE B:194 , ASN B:195 , GLY B:222 , GLY B:223 , VAL B:226 , CYS B:249 , GLY B:250 , GLY B:251 , GLY B:272 , THR B:273 , SO4 B:403 , HOH B:504 , HOH B:508 , HOH B:514 , HOH B:515BINDING SITE FOR RESIDUE FMN B 402
11BC2SOFTWARELYS B:44 , ASN B:68 , MET B:70 , GLY B:71 , LEU B:72 , CYS B:131 , ASN B:133 , FMN B:402 , HOH B:501BINDING SITE FOR RESIDUE SO4 B 403
12BC3SOFTWARELEU A:227 , LEU A:231 , HOH A:613 , VAL B:202 , ILE B:203 , HOH B:712 , HOH B:750BINDING SITE FOR RESIDUE GOL B 404
13BC4SOFTWARETHR B:25 , ARG B:51 , PRO B:73 , ASN B:74 , ASN B:75 , HOH B:569 , HOH B:648 , HOH B:709BINDING SITE FOR RESIDUE SO4 B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EF9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:56 -Pro A:57
2Cys A:193 -Ile A:194
3Thr B:56 -Pro B:57
4Cys B:193 -Ile B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EF9)

(-) Exons   (0, 0)

(no "Exon" information available for 4EF9)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ef9a_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ef9 A   0 SMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   


Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ef9b_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ef9 B   0 SMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EF9)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q4QEW7_LEIMA | Q4QEW7: 3gye 3gz3 3mhu 3mjy 3tjx 3tq0 3tro 4ef8

(-) Related Entries Specified in the PDB File

4ef8