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(-) Description

Title :  CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
 
Authors :  K. L. Barrack, W. N. Hunter
Date :  15 Jan 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Short-Chain Dehydrogenase/Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Khalaf, J. K. Huggan, C. J. Suckling, C. L. Gibson, K. Stewart, F. Giordani, M. P. Barrett, P. E. Wong, K. L. Barrack, W. N. Hunter
Structure-Based Design And Synthesis Of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1.
J. Med. Chem. V. 57 6479 2014
PubMed-ID: 25007262  |  Reference-DOI: 10.1021/JM500483B

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE 1
    Chains: A, D
    EC Number: 1.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
 
Molecule 2 - PTERIDINE REDUCTASE 1
    Chains: B, C
    EC Number: 1.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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
1CSX2Mod. Amino AcidS-OXY CYSTEINE
2GOL1Ligand/IonGLYCEROL
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4XP04Ligand/Ion5-(PHENYLETHYNYL)-4-(PYRROLIDIN-1-YL)-7H-PYRROLO[2,3-D]PYRIMIDIN-2-AMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG 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 , PRO A:204 , GLY A:205 , SER A:207 , XP0 A:1270 , HOH A:2005 , HOH A:2006 , HOH A:2007 , HOH A:2011 , HOH A:2032 , HOH A:2114 , HOH A:2215BINDING SITE FOR RESIDUE NAP A1269
2AC2SOFTWARESER A:95 , PHE A:97 , ASP A:161 , TYR A:174 , LEU A:209 , PRO A:210 , TRP A:221 , NAP A:1269BINDING SITE FOR RESIDUE XP0 A1270
3AC3SOFTWAREARG 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 , PRO B:204 , GLY B:205 , VAL B:206 , SER B:207 , XP0 B:1270 , HOH B:2005 , HOH B:2006 , HOH B:2007 , HOH B:2012 , HOH B:2037 , HOH B:2040 , HOH B:2095 , HOH B:2098 , HOH B:2196BINDING SITE FOR RESIDUE NAP B1269
4AC4SOFTWARESER B:95 , PHE B:97 , TYR B:174 , LEU B:209 , PRO B:210 , TRP B:221 , NAP B:1269BINDING SITE FOR RESIDUE XP0 B1270
5AC5SOFTWAREARG C:14 , ILE C:15 , HIS C:33 , 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 , VAL C:206 , SER C:207 , XP0 C:1270 , HOH C:2005 , HOH C:2006 , HOH C:2007 , HOH C:2014 , HOH C:2033 , HOH C:2037 , HOH C:2093 , HOH C:2184 , HOH C:2185BINDING SITE FOR RESIDUE NAP C1269
6AC6SOFTWARESER C:95 , PHE C:97 , TYR C:174 , VAL C:206 , LEU C:209 , PRO C:210 , TRP C:221 , NAP C:1269 , HOH C:2135BINDING SITE FOR RESIDUE XP0 C1270
7AC7SOFTWAREARG D:14 , ILE D:15 , HIS D:33 , 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 , XP0 D:1270 , HOH D:2005 , HOH D:2006 , HOH D:2007 , HOH D:2014 , HOH D:2016 , HOH D:2038 , HOH D:2111 , HOH D:2180BINDING SITE FOR RESIDUE NAP D1269
8AC8SOFTWARESER D:95 , PHE D:97 , TYR D:174 , VAL D:206 , LEU D:209 , MET D:213 , TRP D:221 , NAP D:1269BINDING SITE FOR RESIDUE XP0 D1270
9AC9SOFTWARELEU D:208 , LEU D:209 , GLU D:231 , ALA D:232 , SER D:233 , HOH D:2165BINDING SITE FOR RESIDUE GOL D1271

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CLO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CLO)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               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.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clo A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGKTVETQVAELIGTNAIAPFLLTMSFAQRQSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  ||   119       129       139  ||   157       167       177       187       197       207       217       227       237       247       257       267 
                                                                                                                                104|                          142|                                                                                                                     
                                                                                                                                 113                           151                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               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.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4clo B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGKTVETQVAELIGTNAIAPFLLTMSFAQRQTSSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  ||   119       129       139  ||   156       166 |     176       186       196       206       216       226       236       246       256       266  
                                                                                                                                104|                          142|               168-CSX                                                                                                
                                                                                                                                 113                           150                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clo C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGKTVETQVAELIGTNAIAPFLLTMSFAQRQSSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  ||   119       129       139  ||   157       167|      177       187       197       207       217       227       237       247       257       267 
                                                                                                                                104|                          142|              168-CSX                                                                                                
                                                                                                                                 113                           151                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               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.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clo D   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|                                                                                                                    
                                                                                                                                113                           152
   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 4CLO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4clr 4clx 4cm1 4cm3 4cm4 4cm5 4cm6 4cm7 4cm8 4cm9 4cma 4cmb 4cmc 4cme 4cmg 4cmi 4cmj 4cmk 4wcd 4wcf 5izc 5jcj 5jcx 5jdc 5jdi 5k6a

(-) Related Entries Specified in the PDB File

4cl8 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cld CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cle CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4clh CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4clr CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR