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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NEQ0130
 
Authors :  J. R. Rocha, D. K. Inaoka, J. Cheleski, T. Shiba, S. Harada, C. A. Montana
Date :  15 Oct 15  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  T. Cruzi, Dihydroorotate Dehydrogenase, Covalent Inhibitor, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Rocha, J. Cheleski, D. K. Inaoka, L. A. Avelar, J. F. R. Ribeiro, H. J. Wiggers, S. Albuquerque, T. Shiba, S. Harada, K. Kita, A. B. F. Silva, C. A. Montanari
Exploring Trypanosoma Cruzi Dihydroorotate Dehydrogenase Active Site Plasticity For The Discovery Of Potent And Selective Inhibitors With Trypanocidal Activity
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (FUMARATE)
    ChainsA, B
    EC Number1.3.98.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET SUMO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePYRD,PYR4
    Organism ScientificTRYPANOSOMA CRUZI STRAIN CL BRENER
    Organism Taxid353153
    StrainCL BRENER
    SynonymDHODEHASE,DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric/Biological Unit (5, 30)
No.NameCountTypeFull Name
15LM2Ligand/Ion5-[(E)-3-THIOPHEN-2-YLPROP-2-ENYLIDENE]-1,3-DIAZINANE-2,4,6-TRIONE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL13Ligand/IonGLYCEROL
5NCO2Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:44 , CYS A:45 , ASN A:67 , MET A:69 , GLY A:70 , LEU A:71 , PRO A:72 , ASN A:73 , SER A:99 , ASN A:127 , CYS A:130 , ASN A:132 , ASN A:194 , SER A:195 , FMN A:409 , HOH A:569binding site for residue 5LM A 401
02AC2SOFTWAREILE A:171 , ARG A:239 , HOH A:599 , HOH A:671 , LYS B:214 , GLN B:215 , PHE B:217 , HOH B:509 , HOH B:608binding site for residue GOL A 402
03AC3SOFTWAREPHE A:61 , ASP A:203 , HOH A:562 , HOH A:612 , HOH A:669binding site for residue GOL A 403
04AC4SOFTWAREGOL A:408 , HOH A:524 , HOH A:543binding site for residue GOL A 404
05AC5SOFTWAREASP A:175 , THR A:176 , HOH A:645 , LEU B:80 , ARG B:112 , HOH B:573 , HOH B:612binding site for residue GOL A 405
06AC6SOFTWARELEU A:4 , ASN A:5 , GLU A:302 , ARG A:305 , HOH A:552 , HOH A:574 , HOH A:666 , LYS B:3 , ASN B:5binding site for residue GOL A 406
07AC7SOFTWARETYR A:237 , PRO A:241binding site for residue GOL A 407
08AC8SOFTWARELEU A:22 , ASP A:28 , GOL A:404 , HOH A:502 , HOH A:503 , HOH A:511 , HOH A:537 , HOH A:704binding site for residue GOL A 408
09AC9SOFTWAREALA A:18 , ALA A:19 , GLY A:20 , LYS A:43 , SER A:44 , ASN A:67 , ASN A:127 , LYS A:164 , VAL A:193 , ASN A:194 , SER A:195 , GLY A:221 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , 5LM A:401 , HOH A:522 , HOH A:548 , HOH A:553 , HOH A:564binding site for residue FMN A 409
10AD1SOFTWARELEU A:63 , LYS A:223 , HOH A:520 , HOH A:531 , HOH A:593 , LEU B:63binding site for residue EDO A 410
11AD2SOFTWARELEU A:74 , GLY A:75 , ASP A:77 , PHE A:78 , HOH A:518binding site for residue EDO A 411
12AD3SOFTWARETYR A:252 , ALA A:273 , GLU A:276 , GLU A:277 , ARG A:284 , HOH A:514 , HOH A:521 , HOH A:561binding site for residue EDO A 412
13AD4SOFTWAREVAL A:10 , PRO A:93 , HOH A:506 , HOH A:525 , ARG B:299 , THR B:300binding site for residue EDO A 413
14AD5SOFTWAREGLY A:278 , PRO A:279 , HOH A:643 , GLY B:278 , PRO B:279 , NCO B:409 , HOH B:656binding site for residue EDO A 414
15AD6SOFTWARELYS A:214 , GLN A:215 , PHE A:217 , ILE B:171 , ARG B:238 , ARG B:239 , HOH B:543 , HOH B:620 , HOH B:699binding site for residue GOL B 402
16AD7SOFTWAREHIS A:173 , TYR B:141 , TYR B:168 , PHE B:169 , HIS B:173 , HOH B:502 , HOH B:505binding site for residue GOL B 403
17AD8SOFTWAREARG A:112 , THR B:176 , HOH B:542binding site for residue GOL B 404
18AD9SOFTWAREILE A:171 , ALA A:172 , HOH A:576 , PRO B:115 , GLY B:135 , PRO B:137 , EDO B:413 , HOH B:506 , HOH B:522 , HOH B:529binding site for residue GOL B 405
19AE1SOFTWARETYR B:58 , HOH B:508 , HOH B:515binding site for residue GOL B 406
20AE2SOFTWARECYS A:31 , ALA A:34 , SER A:35 , CYS B:31 , ALA B:34 , SER B:35 , HOH B:615 , HOH B:638binding site for residue GOL B 407
21AE3SOFTWAREALA B:18 , ALA B:19 , GLY B:20 , LYS B:43 , SER B:44 , ASN B:67 , ASN B:127 , LYS B:164 , VAL B:193 , ASN B:194 , GLY B:221 , GLY B:222 , ILE B:225 , CYS B:248 , GLY B:249 , GLY B:250 , GLY B:271 , THR B:272 , 5LM B:401 , HOH B:526 , HOH B:537 , HOH B:553 , HOH B:618binding site for residue FMN B 408
22AE4SOFTWAREGLN A:275 , GLU A:276 , GLY A:278 , EDO A:414 , GLN B:275 , GLU B:276 , GLY B:278 , HOH B:689 , HOH B:692binding site for residue NCO B 409
23AE5SOFTWAREASP A:203 , ASP B:203binding site for residue NCO B 410
24AE6SOFTWAREHOH A:531 , LEU B:63 , LYS B:223 , HOH B:636 , HOH B:747binding site for residue EDO B 411
25AE7SOFTWAREALA B:273 , GLU B:276 , GLU B:277 , ARG B:284 , HOH B:524 , HOH B:533 , HOH B:575binding site for residue EDO B 412
26AE8SOFTWAREARG B:111 , ALA B:114 , PRO B:115 , ALA B:156 , GOL B:405 , HOH B:517binding site for residue EDO B 413
27AE9SOFTWAREPHE B:61 , HOH B:511 , HOH B:605 , HOH B:635binding site for residue EDO B 414
28AF1SOFTWARETHR B:25 , LEU B:74 , HOH B:504 , HOH B:528 , HOH B:550 , HOH B:591 , HOH B:599binding site for residue EDO B 415
29AF2SOFTWAREARG B:30 , THR B:33 , TYR B:82 , HIS B:87 , ASP B:88 , HOH B:597binding site for residue EDO B 416
30AF3SOFTWARESER B:44 , CYS B:45 , THR B:46 , ASN B:67 , MET B:69 , GLY B:70 , LEU B:71 , PRO B:72 , ASN B:73 , SER B:99 , ASN B:127 , SER B:129 , PRO B:131 , ASN B:132 , GLN B:138 , ASN B:194 , SER B:195 , FMN B:408 , HOH B:551 , HOH B:559 , HOH B:627binding site for Di-peptide 5LM B 401 and CYS B 130

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1 -B:1

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:55 -Pro A:56
2Cys A:192 -Val A:193
3Glu B:55 -Pro B:56
4Cys B:192 -Val B:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EA9)

(-) Exons   (0, 0)

(no "Exon" information available for 5EA9)

(-) 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....ee................eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ea9 A   0 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee...eee.......hhhhhhhhhhh....ee................eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ea9 B   0 MCLKLNLLDHVFANPFMNAAGVLCSTEEDLRCMTASSSGALVSKSCTSAPRDGNPEPRYMAFPLGSINSMGLPNLGFDFYLKYASDLHDYSKKPLFLSISGLSVEENVAMVRRLAPVAQEKGVLLELNLSCPNVPGKPQVAYDFEAMRTYLQQVSLAYGLPFGVKMPPYFDIAHFDTAAAVLNEFPLVKFVTCVNSVGNGLVIDAESESVVIKPKQGFGGLGGKYILPTALANVNAFYRRCPDKLVFGCGGVYSGEDAFLHILAGASMVQVGTALQEEGPGIFTRLEDELLEIMARKGYRTLEEFRGRVKTIE 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  (0, 0)

(no "SCOP Domain" information available for 5EA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EA9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRD_TRYCC | Q4D3W22djl 2djx 2e68 2e6a 2e6d 2e6f 3c3n 3w1a 3w1l 3w1m 3w1n 3w1p 3w1q 3w1r 3w1t 3w1u 3w1x 3w22 3w23 3w2j 3w2k 3w2l 3w2m 3w2n 3w2u 3w3o 3w6y 3w70 3w71 3w72 3w73 3w74 3w75 3w76 3w7c 3w7d 3w7e 3w7g 3w7h 3w7i 3w7j 3w7k 3w7l 3w7m 3w7n 3w7o 3w7p 3w7q 3w83 3w84 3w85 3w86 3w87 3w88 4jd4 4jdb 5e93

(-) Related Entries Specified in the PDB File

5e93