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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NEQ0071
 
Authors :  J. R. Rocha, D. K. Inaoka, J. Cheleski, T. Shiba, S. Harada, C. A. Montana
Date :  14 Oct 15  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
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)
    Chains: A, B
    EC Number: 1.3.98.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYRD,PYR4
    Organism Scientific: TRYPANOSOMA CRUZI STRAIN CL BRENER
    Organism Taxid: 353153
    Strain: CL BRENER
    Synonym: DHODEHASE,DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 45)

Asymmetric/Biological Unit (7, 45)
No.NameCountTypeFull Name
15LL2Ligand/Ion5-[(E)-3-(FURAN-2-YL)PROP-2-ENYLIDENE]-1,3-DIAZINANE-2,4,6-TRIONE
2CAC2Ligand/IonCACODYLATE ION
3EDO23Ligand/Ion1,2-ETHANEDIOL
4FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
5GOL12Ligand/IonGLYCEROL
6NCO3Ligand/IonCOBALT HEXAMMINE(III)
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (45, 45)

Asymmetric Unit (45, 45)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:44 , CYS A:45 , ASN A:67 , MET A:69 , GLY A:70 , LEU A:71 , ASN A:73 , SER A:99 , ASN A:127 , CYS A:130 , PRO A:131 , ASN A:132 , ASN A:194 , SER A:195 , FMN A:408 , HOH A:528 , HOH A:713binding site for residue 5LL A 401
02AC2SOFTWAREILE A:171 , ARG A:239 , HOH A:524 , HOH A:653 , LYS B:214 , PHE B:217 , HOH B:630binding site for residue GOL A 402
03AC3SOFTWARETYR A:58 , MET A:69 , CAC A:421 , HOH A:512 , HOH A:517 , HOH A:707binding site for residue GOL A 403
04AC4SOFTWARETHR A:176 , HOH A:623 , LEU B:80 , ARG B:112 , HOH B:654binding site for residue GOL A 404
05AC5SOFTWAREPRO A:115 , GLY A:135 , PRO A:137 , EDO A:414 , HOH A:535 , HOH A:687 , HOH A:691 , ILE B:171 , ALA B:172 , HOH B:555 , HOH B:575binding site for residue GOL A 405
06AC6SOFTWAREPHE A:61 , TYR A:224 , EDO A:416 , HOH A:503 , HOH A:695binding site for residue GOL A 406
07AC7SOFTWAREVAL A:10 , TYR A:89 , SER A:90 , LYS A:91 , PRO A:93 , EDO A:419 , HOH A:537 , HOH A:542 , HOH A:567binding site for residue GOL A 407
08AC8SOFTWAREALA 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 , GLY A:221 , GLY A:222 , ILE A:225 , CYS A:248 , GLY A:249 , GLY A:250 , GLY A:271 , THR A:272 , 5LL A:401 , HOH A:526 , HOH A:527 , HOH A:553 , HOH A:611binding site for residue FMN A 408
09AC9SOFTWARELYS A:296 , HOH A:648 , HOH A:732 , LYS B:296 , EDO B:415 , HOH B:554binding site for residue NCO A 409
10AD1SOFTWARELYS A:223 , HOH A:693 , HOH A:772 , HOH A:795 , HOH B:506binding site for residue EDO A 410
11AD2SOFTWAREGLU A:277 , ARG A:284 , HOH A:530 , HOH A:634 , HOH A:640 , HOH A:674 , GLU B:27 , HOH B:550binding site for residue EDO A 411
12AD3SOFTWARETYR A:252 , ALA A:273 , GLU A:276 , GLU A:277 , ARG A:284 , HOH A:515 , HOH A:555 , HOH A:627binding site for residue EDO A 412
13AD4SOFTWAREGLU A:255 , ARG A:295 , HOH A:608 , ALA B:204 , GLU B:205binding site for residue EDO A 413
14AD5SOFTWAREARG A:111 , ALA A:114 , PRO A:115 , ALA A:156 , TYR A:157 , GOL A:405 , HOH A:507 , HOH A:620binding site for residue EDO A 414
15AD6SOFTWARESER A:208 , THR B:310 , HOH B:734binding site for residue EDO A 415
16AD7SOFTWAREVAL A:201 , ILE A:202 , GOL A:406 , HOH A:573 , LEU B:226 , LEU B:230 , LEU B:259 , HOH B:548binding site for residue EDO A 416
17AD8SOFTWARETHR A:25 , HOH A:533 , HOH A:547 , HOH A:582 , HOH A:606 , HOH A:610 , HOH A:680binding site for residue EDO A 417
18AD9SOFTWAREARG A:238 , GLY A:306 , VAL A:308 , HOH A:538binding site for residue EDO A 418
19AE1SOFTWAREALA A:12 , SER A:36 , SER A:37 , LYS A:91 , GOL A:407 , HOH A:504 , HOH A:542binding site for residue EDO A 419
20AE2SOFTWAREGLU A:26 , GLU A:27 , ARG A:30 , HOH A:763 , THR B:283 , ARG B:284 , ASP B:287 , HOH B:511binding site for residue EDO A 420
21AE3SOFTWAREASP A:28 , GOL A:403 , HOH A:508 , HOH A:531 , HOH A:595 , HOH A:785binding site for residue CAC A 421
22AE4SOFTWAREHOH A:574 , HOH A:587 , ASP B:28 , GOL B:403 , HOH B:519 , HOH B:589binding site for residue CAC A 422
23AE5SOFTWARELYS A:214 , GLN A:215 , PHE A:217 , HOH A:521 , HOH A:691 , ILE B:171 , ARG B:239 , HOH B:533 , HOH B:649binding site for residue GOL B 402
24AE6SOFTWARECAC A:422 , TYR B:58 , MET B:69 , HOH B:514 , HOH B:515binding site for residue GOL B 403
25AE7SOFTWARELEU A:80 , ARG A:112 , HOH A:635 , HOH A:637 , ASP B:175 , THR B:176 , HOH B:736binding site for residue GOL B 404
26AE8SOFTWAREHIS A:173 , TYR B:141 , TYR B:168 , PHE B:169 , HIS B:173 , HOH B:508 , HOH B:517 , HOH B:521binding site for residue GOL B 405
27AE9SOFTWAREASN A:5 , LEU B:4 , ASN B:5 , ARG B:305 , HOH B:577 , HOH B:581 , HOH B:648 , HOH B:679binding site for residue GOL B 406
28AF1SOFTWARECYS A:31 , ALA A:34 , SER A:35 , CYS B:31 , ALA B:34 , SER B:35 , HOH B:633 , HOH B:662binding site for residue GOL B 407
29AF2SOFTWAREALA 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 , 5LL B:401 , HOH B:528 , HOH B:532 , HOH B:568 , HOH B:585binding site for residue FMN B 408
30AF3SOFTWAREGLN A:275 , GLU A:276 , GLY A:278 , GLN B:275 , GLU B:276 , GLY B:278 , PEG B:423 , HOH B:729binding site for residue NCO B 409
31AF4SOFTWAREASP A:203 , GLU A:205 , ASP B:203 , GLU B:205 , HOH B:503binding site for residue NCO B 410
32AF5SOFTWAREGLU A:205 , GLU B:255 , ARG B:295 , LYS B:296binding site for residue EDO B 411
33AF6SOFTWARELEU A:63 , LYS B:223 , HOH B:506 , HOH B:625 , HOH B:741binding site for residue EDO B 412
34AF7SOFTWAREARG B:238 , GLY B:306 , VAL B:308 , THR B:310 , HOH B:547 , HOH B:608 , HOH B:615binding site for residue EDO B 413
35AF8SOFTWARELEU B:74 , GLY B:75 , ASP B:77 , PHE B:78 , EDO B:421 , HOH B:523 , HOH B:558binding site for residue EDO B 414
36AF9SOFTWAREGLU A:205 , LYS A:309 , NCO A:409 , GLU B:205 , SER B:206 , GLU B:207 , HOH B:554binding site for residue EDO B 415
37AG1SOFTWARETYR B:252 , ALA B:273 , GLU B:276 , GLU B:277 , ARG B:284 , EDO B:417 , HOH B:507 , HOH B:520 , HOH B:524binding site for residue EDO B 416
38AG2SOFTWARELYS B:223 , TYR B:252 , EDO B:416 , HOH B:518 , HOH B:524binding site for residue EDO B 417
39AG3SOFTWAREPRO B:185 , LEU B:186 , HOH B:502 , HOH B:728binding site for residue EDO B 418
40AG4SOFTWAREARG A:299 , THR A:300 , VAL B:10 , LYS B:91 , HOH B:501 , HOH B:526 , HOH B:592binding site for residue EDO B 419
41AG5SOFTWAREARG B:30 , THR B:33 , TYR B:82 , HIS B:87 , ASP B:88 , HOH B:688binding site for residue EDO B 420
42AG6SOFTWAREGLU A:183 , PRO B:49 , ASP B:77 , EDO B:414 , HOH B:513binding site for residue EDO B 421
43AG7SOFTWAREPHE B:61 , HOH B:510 , HOH B:626 , HOH B:686 , HOH B:726binding site for residue EDO B 422
44AG8SOFTWARELEU A:22 , CYS A:31 , GLY A:278 , PRO A:279 , HOH A:628 , HOH A:658 , LEU B:22 , GLU B:277 , GLY B:278 , PRO B:279 , GLY B:280 , NCO B:409 , HOH B:658 , HOH B:680binding site for residue PEG B 423
45AG9SOFTWARESER B:44 , ASN B:67 , MET B:69 , GLY B:70 , LEU B:71 , 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:599 , HOH B:613 , HOH B:675 , HOH B:720binding site for Di-peptide 5LL 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 5E93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E93)

(-) Exons   (0, 0)

(no "Exon" information available for 5E93)

(-) 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....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e93 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....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e93 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)
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  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 5E93)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E93)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  5e93
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRD_TRYCC | Q4D3W2: 2djl 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 5ea9

(-) Related Entries Specified in the PDB File

5ea9