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(-) Description

Title :  TRYPANOSOMA BRUCEI PTR1 IN COMPLEX WITH INHIBITOR NP-13 (HESPERETIN)
 
Authors :  S. Mangani, C. Pozzi, F. Di Pisa, G. Landi, L. Dello Iacono
Date :  16 Apr 16  (Deposition) - 17 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Trypanosoma Brucei, Pteridine Reductase, Oxydoreductase, Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Borsari, R. Luciani, C. Pozzi, I. Poehner, S. Henrich, M. Trande, A. Cordeiro-Da-Silva, N. Santarem, C. Baptista, A. Tait, F. Di Pisa, L. Dello Iacono, G. Landi, S. Gul, M. Wolf, M. Kuzikov, B. Ellinger, J. Reinshagen, G. Witt, P. Gribbon, M. Kohler, O. Keminer, B. Behrens, L. Costantino, P. Tejera Nevado, E. Bifeld, J. Eick, J. Clos, J. Torrado, M. D. Jimenez-Anton, M. J. Corral, J. M. Alunda, F. Pellati R. C. Wade, S. Ferrari, S. Mangani, M. P. Costi
Profiling Of Flavonol Derivatives For The Development Of Antitrypanosomatidic Drugs.
J. Med. Chem. V. 59 7598 2016
PubMed-ID: 27411733  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00698

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE
    Chains: A, B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PTR1
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
 
Molecule 2 - PTERIDINE REDUCTASE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PTR1
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
16JP4Ligand/Ion(2S)-5,7-DIHYDROXY-2-(3-HYDROXY-4-METHOXYPHENYL)-2,3-DIHYDRO-4H-1-BENZOPYRAN-4-ONE
2ACT2Ligand/IonACETATE ION
3CSX4Mod. Amino AcidS-OXY CYSTEINE
4GOL1Ligand/IonGLYCEROL
5NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:14 , ILE A:15 , TYR A:34 , HIS A:35 , ASN A:36 , SER A:37 , ALA A:61 , ASP A:62 , LEU A:63 , THR A:64 , ASN A:93 , ALA A:94 , SER A:95 , THR A:126 , LEU A:159 , CYS A:160 , TYR A:174 , LYS A:178 , GLY A:205 , SER A:207 , LEU A:208 , 6JP A:302 , HOH A:402 , HOH A:407 , HOH A:414 , HOH A:447binding site for residue NAP A 301
02AC2SOFTWAREARG A:14 , SER A:95 , PHE A:97 , ASP A:161 , MET A:163 , GLN A:166 , CSX A:168 , TYR A:174 , LEU A:208 , LEU A:209 , PRO A:210 , TRP A:221 , NAP A:301 , HOH A:451 , HIS D:267binding site for residue 6JP A 302
03AC3SOFTWARELYS A:13 , ARG A:14 , HOH A:416binding site for residue ACT A 303
04AC4SOFTWAREARG B:14 , ILE B:15 , TYR B:34 , HIS B:35 , ASN B:36 , SER B:37 , ALA B:61 , ASP B:62 , LEU B:63 , THR B:64 , ASN B:93 , ALA B:94 , SER B:95 , THR B:126 , LEU B:159 , CYS B:160 , TYR B:174 , LYS B:178 , PRO B:204 , GLY B:205 , SER B:207 , LEU B:208 , 6JP B:302 , HOH B:408 , HOH B:420 , HOH B:436 , HOH B:444 , HOH B:476binding site for residue NAP B 301
05AC5SOFTWAREARG B:14 , SER B:95 , PHE B:97 , ASP B:161 , MET B:163 , GLN B:166 , PRO B:167 , CSX B:168 , TYR B:174 , LEU B:208 , PRO B:210 , NAP B:301 , HOH B:466binding site for residue 6JP B 302
06AC6SOFTWAREGLY C:10 , ARG C:14 , ILE C:15 , TYR C:34 , HIS C:35 , ASN C:36 , SER C:37 , ASP C:62 , LEU C:63 , THR C:64 , ASN C:93 , ALA C:94 , SER C:95 , THR C:126 , LEU C:159 , CYS C:160 , ASP C:161 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , VAL C:206 , SER C:207 , 6JP C:302 , HOH C:421 , HOH C:425binding site for residue NAP C 301
07AC7SOFTWAREHIS B:267 , ARG C:14 , SER C:95 , PHE C:97 , ASP C:161 , MET C:163 , GLN C:166 , CSX C:168 , TYR C:174 , LEU C:209 , PRO C:210 , NAP C:301binding site for residue 6JP C 302
08AC8SOFTWARETYR B:34 , VAL B:58 , VAL C:57 , VAL C:58binding site for residue ACT C 303
09AC9SOFTWAREALA B:45 , ASP B:46 , VAL B:57 , VAL B:58 , TYR C:34 , VAL C:58 , OCS C:59 , GLN C:60binding site for residue GOL C 304
10AD1SOFTWAREARG D:14 , ILE D:15 , TYR D:34 , HIS D:35 , ASN D:36 , SER D:37 , ALA D:61 , ASP D:62 , LEU D:63 , THR D:64 , ASN D:93 , ALA D:94 , SER D:95 , THR D:126 , LEU D:159 , CYS D:160 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , VAL D:206 , SER D:207 , LEU D:208 , 6JP D:302 , HOH D:408 , HOH D:422 , HOH D:437binding site for residue NAP D 301
11AD2SOFTWAREHIS A:267 , ARG D:14 , SER D:95 , PHE D:97 , ASP D:161 , MET D:163 , GLN D:166 , CSX D:168 , TYR D:174 , LEU D:208 , LEU D:209 , PRO D:210 , NAP D:301 , HOH D:415binding site for residue 6JP D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JDC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JDC)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdc A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVGKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    120       130       140 ||    159       169       179       189       199       209       219       229       239       249       259         
                                                                                                                               103|                          142|             168-CSX                                                                                                
                                                                                                                                113                           152                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jdc B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVKTVETQVAELIGTNAIAPFLLTMSFAQRQNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    121       131       141||     161      |171       181       191       201       212       222       232       242       252       262      
                                                                                                                               103|                         142|            168-CSX                                   210|                                                        
                                                                                                                                114                          153                                                       212                                                        


Chain C from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdc C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVKTVETQVAELIGTNAIAPFLLTMSFAQRQNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLPEEKDKWRRKVPLGRRSAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51       |61        71        81        91       101 ||    121       131       141||     161      |171       181       191       201     ||217       227  ||   239       249       259         
                                                                                    59-OCS                                     103|                         142|            168-CSX                                207|||           230|                                   
                                                                                                                                114                          153                                                    209||            233                                   
                                                                                                                                                                                                                     210|                                                  
                                                                                                                                                                                                                      216                                                  


Chain D from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdc D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    121       131       141||     160       170       180       190       200       210       220       230       240       250       260        
                                                                                                                               103|                         142|             168-CSX                                                                                                
                                                                                                                                114                          152
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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 5JDC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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        O76290_TRYBB | O76290: 2c7v 2vz0 2wd7 2wd8 2x9g 2x9n 2x9v 2yhu 3bmc 3bmn 3bmo 3bmq 3gn1 3gn2 3mcv 4cl8 4cld 4cle 4clh 4clo 4clr 4clx 4cm1 4cm3 4cm4 4cm5 4cm6 4cm7 4cm8 4cm9 4cma 4cmb 4cmc 4cme 4cmg 4cmi 4cmj 4cmk 4wcd 4wcf 5izc 5jcj 5jcx 5jdi 5k6a

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