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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 :  1.81
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Ptr1, 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
    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
 
Molecule 2 - PTERIDINE REDUCTASE 1
    Chains: 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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
14NR4Ligand/Ion5-(4-FLUOROPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-2,4-DIAMINE
2ACT2Ligand/IonACETATE ION
3CSX1Mod. Amino AcidS-OXY CYSTEINE
4GOL1Ligand/IonGLYCEROL
5NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) 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 , PRO A:204 , GLY A:205 , SER A:207 , LEU A:208 , 4NR A:1270 , HOH A:2007 , HOH A:2008 , HOH A:2009 , HOH A:2012 , HOH A:2014 , HOH A:2034 , HOH A:2037 , HOH A:2100 , HOH A:2104 , HOH A:2122 , HOH A:2219BINDING SITE FOR RESIDUE NAP A1269
02AC2SOFTWAREARG 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 , 4NR B:1270 , HOH B:2008 , HOH B:2009 , HOH B:2010 , HOH B:2013 , HOH B:2018 , HOH B:2040 , HOH B:2043 , HOH B:2094 , HOH B:2097 , HOH B:2110 , HOH B:2200 , HOH B:2201BINDING SITE FOR RESIDUE NAP B1269
03AC3SOFTWAREARG 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 , 4NR C:1270 , HOH C:2005 , HOH C:2006 , HOH C:2007 , HOH C:2014 , HOH C:2030 , HOH C:2033 , HOH C:2076 , HOH C:2078 , HOH C:2088 , HOH C:2116 , HOH C:2154 , HOH C:2155BINDING SITE FOR RESIDUE NAP C1269
04AC4SOFTWAREARG 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 , 4NR D:1270 , HOH D:2002 , HOH D:2003 , HOH D:2004 , HOH D:2010 , HOH D:2028 , HOH D:2034 , HOH D:2076 , HOH D:2079 , HOH D:2117 , HOH D:2140BINDING SITE FOR RESIDUE NAP D1269
05AC5SOFTWARESER A:95 , PHE A:97 , ASP A:161 , TYR A:174 , LEU A:209 , PRO A:210 , MET A:213 , TRP A:221 , NAP A:1269 , GOL A:1271 , HOH A:2164BINDING SITE FOR RESIDUE 4NR A1270
06AC6SOFTWARESER B:95 , PHE B:97 , TYR B:174 , LEU B:209 , PRO B:210 , MET B:213 , TRP B:221 , NAP B:1269 , HOH B:2018 , HOH B:2151BINDING SITE FOR RESIDUE 4NR B1270
07AC7SOFTWAREARG C:14 , SER C:95 , PHE C:97 , ASP C:161 , TYR C:174 , LEU C:209 , PRO C:210 , MET C:213 , TRP C:221 , NAP C:1269 , HOH C:2014 , HOH C:2116BINDING SITE FOR RESIDUE 4NR C1270
08AC8SOFTWARESER D:95 , PHE D:97 , ASP D:161 , TYR D:174 , LEU D:209 , PRO D:210 , MET D:213 , TRP D:221 , NAP D:1269 , HOH D:2010BINDING SITE FOR RESIDUE 4NR D1270
09AC9SOFTWAREALA B:212 , MET B:213 , GLY B:214 , GLU B:215 , HOH B:2155 , HOH B:2160 , HOH B:2163BINDING SITE FOR RESIDUE ACT B1271
10BC1SOFTWAREALA B:56 , VAL B:58 , HOH B:2054 , ARG C:82 , HOH C:2052BINDING SITE FOR RESIDUE ACT B1272
11BC2SOFTWARECSX A:168 , PRO A:210 , TRP A:221 , 4NR A:1270 , HOH A:2220 , HOH A:2221BINDING SITE FOR RESIDUE GOL A1271

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CM4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CM4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CM4)

(-) Exons   (0, 0)

(no "Exon" information available for 4CM4)

(-) 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.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cm4 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|              168-CSX                                                                                                
                                                                                                                                 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....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
                 4cm4 B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVGKTVETQVAELIGTNAIAPFLLTMSFAQRQKSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    120       130       140  ||   157       167       177       187       197       207       217       227       237       247       257       267 
                                                                                                                               103|                           143|                                                                                                                     
                                                                                                                                113                            151                                                                                                                     


Chain C 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.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cm4 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|                                                                                                                     
                                                                                                                                 113                           151                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               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
                 4cm4 D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVGKTVETQVAELIGTNAIAPFLLTMSFAQRQSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 ||    120       130       140 ||    158       168       178       188       198       208       218       228       238       248       258       268
                                                                                                                               103|                          142|                                                                                                                     
                                                                                                                                113                           151
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(no "SCOP Domain" information available for 4CM4)

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(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CM4)

(-) 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 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
4clo 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
4clx CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm1 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm3 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm5 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm6 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm7 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm8 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cm9 CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cma CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmb CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmc CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cme CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmg CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmi CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmj CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR
4cmk CRYSTAL STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR AND INHIBITOR