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(-) Description

Title :  TRYPANOSOMA BRUCEI PTR1 IN COMPLEX WITH COFACTOR AND INHIBITOR NMT-H024 (COMPOUND 2)
 
Authors :  G. Landi, C. Pozzi, F. Di Pisa, L. Dello Lacono, S. Mangani
Date :  16 Apr 16  (Deposition) - 17 Aug 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
16JO3Ligand/Ion3,6-DIHYDROXY-2-(3-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE
2ACT3Ligand/IonACETATE ION
3CSX1Mod. Amino AcidS-OXY CYSTEINE
4NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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 , ASP A:161 , TYR A:174 , LYS A:178 , GLY A:205 , SER A:207 , LEU A:208 , 6JO A:304 , HOH A:418 , HOH A:420 , HOH A:427 , HOH A:429 , HOH A:432 , HOH A:463 , HOH A:508 , HOH A:518 , HOH A:557 , HOH A:558 , HOH A:564binding site for residue NAP A 301
02AC2SOFTWARELYS A:13 , ARG A:14 , ARG A:17 , HOH A:475binding site for residue ACT A 302
03AC3SOFTWAREPRO A:4 , THR A:26binding site for residue ACT A 303
04AC4SOFTWAREARG A:14 , SER A:95 , PHE A:97 , TYR A:174 , GLY A:205 , VAL A:206 , LEU A:208 , LEU A:209 , PRO A:210 , TRP A:221 , NAP A:301 , HOH A:411 , HOH A:557binding site for residue 6JO A 304
05AC5SOFTWAREARG 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 , ASP B:161 , TYR B:174 , LYS B:178 , GLY B:205 , SER B:207 , LEU B:208 , 6JO B:302 , HOH B:420 , HOH B:427 , HOH B:428 , HOH B:433 , HOH B:459 , HOH B:461 , HOH B:535 , HOH B:547 , HOH B:555binding site for residue NAP B 301
06AC6SOFTWAREARG B:14 , SER B:95 , PHE B:97 , TYR B:174 , GLY B:205 , VAL B:206 , LEU B:208 , LEU B:209 , PRO B:210 , TRP B:221 , NAP B:301 , HOH B:429 , HOH B:531binding site for residue 6JO B 302
07AC7SOFTWAREARG C:14 , ILE C:15 , TYR C:34 , HIS C:35 , ASN C:36 , SER C:37 , ALA C:61 , 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 , SER C:207 , HOH C:401 , HOH C:405 , HOH C:427 , HOH C:440 , HOH C:493 , HOH C:508 , HOH C:512binding site for residue NAP C 301
08AC8SOFTWARETYR B:34 , VAL C:57 , VAL C:58binding site for residue ACT C 302
09AC9SOFTWAREARG 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 , ASP D:161 , TYR D:174 , LYS D:178 , GLY D:205 , SER D:207 , LEU D:208 , 6JO D:302 , HOH D:412 , HOH D:419 , HOH D:422 , HOH D:424 , HOH D:436 , HOH D:438 , HOH D:517 , HOH D:550 , HOH D:551 , HOH D:561 , HOH D:563binding site for residue NAP D 301
10AD1SOFTWAREARG D:14 , SER D:95 , PHE D:97 , TYR D:174 , GLY D:205 , VAL D:206 , LEU D:208 , LEU D:209 , PRO D:210 , TRP D:221 , NAP D:301 , HOH D:428 , HOH D:547 , HOH D:550binding site for residue 6JO D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JDI)

(-) 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.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdi A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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         
                                                                                                                                104|                         142|                                                                                                                    
                                                                                                                                 114                          152                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdi B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVKTVETQVAELIGTNAIAPFLLTMSFAQRQNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    121       131       141||     161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                               103|                         142|                                                                                                                   
                                                                                                                                114                          153                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               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....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jdi C   3 APAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQKTVETQVAELIGTNAIAPFLLTMSFAQRQNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    12        22        32        42        52        62        72        82        92       102 ||    121       131       141||     161      |171       181       191       201     ||218       228       238       248       258       268
                                                                                                                               104|                         142|            168-CSX                                207|                                                     
                                                                                                                                114                          153                                                    215                                                     


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.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jdi D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQKTVETQVAELIGTNAIAPFLLTMSFAQRQNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  ||   120       130       140 ||    160       170       180       190       200       210       220       230       240       250       260        
                                                                                                                                104|                         142|                                                                                                                   
                                                                                                                                 114                          153
   Legend:   → Mismatch (orange background)
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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 5JDI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        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 5jdc 5k6a

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