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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 :  13 Jan 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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, B, C, D
    EC Number: 1.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 5702
    Synonym: PTR1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3OZJ4Ligand/Ion2,4-DIAMINO-6-(3-FORMYLPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:14 , SER A:95 , PHE A:97 , CYS A:168 , TYR A:174 , GLY A:205 , LEU A:209 , PRO A:210 , NAP A:1269 , ACT A:1271 , HOH A:2011 , HOH A:2106 , HOH A:2110BINDING SITE FOR RESIDUE OZJ A1168
02AC2SOFTWAREARG B:14 , SER B:95 , PHE B:97 , CYS B:168 , TYR B:174 , GLY B:205 , PRO B:210 , NAP B:1269 , ACT B:1270 , HOH B:2113 , HOH B:2124BINDING SITE FOR RESIDUE OZJ B1168
03AC3SOFTWAREARG C:14 , SER C:95 , PHE C:97 , ASP C:161 , CYS C:168 , TYR C:174 , GLY C:205 , PRO C:210 , NAP C:1269 , HOH C:2010 , HOH C:2089 , HOH C:2093BINDING SITE FOR RESIDUE OZJ C1168
04AC4SOFTWAREARG D:14 , SER D:95 , PHE D:97 , CYS D:168 , TYR D:174 , GLY D:205 , PRO D:210 , NAP D:1269 , HOH D:2008 , HOH D:2081BINDING SITE FOR RESIDUE OZJ D1168
05AC5SOFTWAREARG 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 , PRO A:204 , GLY A:205 , VAL A:206 , SER A:207 , LEU A:208 , OZJ A:1168 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2008 , HOH A:2024 , HOH A:2027 , HOH A:2093 , HOH A:2178BINDING SITE FOR RESIDUE NAP A1269
06AC6SOFTWAREARG 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 , SER B:207 , LEU B:208 , OZJ B:1168 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2011 , HOH B:2031 , HOH B:2038 , HOH B:2090 , HOH B:2176 , HOH B:2177BINDING SITE FOR RESIDUE NAP B1269
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 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , SER C:207 , LEU C:208 , OZJ C:1168 , HOH C:2003 , HOH C:2004 , HOH C:2005 , HOH C:2010 , HOH C:2025 , HOH C:2069 , HOH C:2071BINDING SITE FOR RESIDUE NAP C1269
08AC8SOFTWAREARG 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 , SER D:207 , LEU D:208 , OZJ D:1168 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2008 , HOH D:2018 , HOH D:2062 , HOH D:2113BINDING SITE FOR RESIDUE NAP D1269
09AC9SOFTWARELYS A:13 , ARG A:14 , ARG A:17 , HOH A:2012 , HOH A:2179BINDING SITE FOR RESIDUE ACT A1270
10BC1SOFTWARETYR B:34 , VAL B:58 , VAL C:57 , VAL C:58 , HOH C:2040BINDING SITE FOR RESIDUE ACT C1270
11BC2SOFTWAREPHE A:97 , MET A:213 , TRP A:221 , OZJ A:1168 , HOH A:2180 , HOH A:2181BINDING SITE FOR RESIDUE ACT A1271
12BC3SOFTWAREMET B:213 , TRP B:221 , OZJ B:1168 , HOH B:2178BINDING SITE FOR RESIDUE ACT B1270

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CL8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CL8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CL8)

(-) Exons   (0, 0)

(no "Exon" information available for 4CL8)

(-) 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..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cl8 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: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.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cl8 B   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 C 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............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cl8 C   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|                                                                                                                    
                                                                                                                                114                          152                                                                                                                    


Chain D 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
                 4cl8 D   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
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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 4CL8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CL8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CL8)

(-) 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 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 5jdi 5k6a

(-) Related Entries Specified in the PDB File

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