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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 :  14 Jan 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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 Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3W8G8Ligand/Ion4-THIOMORPHOLINO-7H-PYRROLO[2,3-D]PYRIMIDIN-2-AMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:14 , ILE A:15 , HIS A:33 , 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 , W8G A:1270 , W8G A:1271 , HOH A:2005 , HOH A:2006 , HOH A:2007 , HOH A:2010 , HOH A:2038 , HOH A:2043 , HOH A:2110 , HOH A:2127 , HOH A:2212 , HOH A:2213BINDING 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 , W8G B:1270 , W8G B:1271 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2037 , HOH B:2040 , HOH B:2044 , HOH B:2102 , HOH B:2199 , HOH B:2200BINDING 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 , W8G C:1270 , W8G C:1271 , HOH C:2004 , HOH C:2005 , HOH C:2006 , HOH C:2028 , HOH C:2085 , HOH C:2087 , HOH C:2161 , HOH C:2162BINDING 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 , VAL D:206 , SER D:207 , W8G D:1270 , W8G D:1271 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2033 , HOH D:2083BINDING SITE FOR RESIDUE NAP D1269
05AC5SOFTWAREARG A:14 , SER A:95 , PHE A:97 , TYR A:174 , PRO A:210 , NAP A:1269 , W8G A:1271BINDING SITE FOR RESIDUE W8G A1270
06AC6SOFTWAREARG B:14 , SER B:95 , PHE B:97 , TYR B:174 , LEU B:208 , PRO B:210 , NAP B:1269 , HOH B:2201BINDING SITE FOR RESIDUE W8G B1270
07AC7SOFTWAREARG C:14 , SER C:95 , PHE C:97 , TYR C:174 , PRO C:210 , NAP C:1269 , W8G C:1271BINDING SITE FOR RESIDUE W8G C1270
08AC8SOFTWAREARG D:14 , SER D:95 , PHE D:97 , TYR D:174 , PRO D:210 , NAP D:1269 , W8G D:1271BINDING SITE FOR RESIDUE W8G D1270
09AC9SOFTWAREPHE A:97 , ASP A:161 , CYS A:168 , GLY A:205 , LEU A:209 , TRP A:221 , NAP A:1269 , W8G A:1270 , HOH A:2148BINDING SITE FOR RESIDUE W8G A1271
10BC1SOFTWAREPHE B:97 , ASP B:161 , MET B:163 , CYS B:168 , GLY B:205 , LEU B:209 , TRP B:221 , NAP B:1269 , HOH B:2140BINDING SITE FOR RESIDUE W8G B1271
11BC2SOFTWAREPHE C:97 , ASP C:161 , MET C:163 , CYS C:168 , GLY C:205 , LEU C:209 , MET C:213 , TRP C:221 , NAP C:1269 , W8G C:1270 , HOH C:2116BINDING SITE FOR RESIDUE W8G C1271
12BC3SOFTWAREPHE D:97 , ASP D:161 , MET D:163 , CYS D:168 , GLY D:205 , LEU D:209 , TRP D:221 , NAP D:1269 , W8G D:1270 , HOH D:2110BINDING SITE FOR RESIDUE W8G D1271
13BC4SOFTWARELYS A:13 , ARG A:14 , ARG A:17 , HOH A:2012 , HOH A:2216BINDING SITE FOR RESIDUE ACT A1272
14BC5SOFTWARETYR B:34 , VAL B:58 , VAL C:57 , VAL C:58BINDING SITE FOR RESIDUE ACT C1272

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val D:211 -Ala D:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CLH)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               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.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4clh A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGKTVETQVAELIGTNAIAPFLLTMSFAQRQKSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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|                           143|                                                                                                                     
                                                                                                                                 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
                 4clh 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.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clh C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVGKTVETQVAELIGTNAIAPFLLTMSFAQRQTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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|                          142|                                                                                                                      
                                                                                                                                113                           150                                                                                                                      


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.............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clh D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVGKTVETQVAELIGTNAIAPFLLTMSFAQRQKSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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|                           143|                                                                                                                    
                                                                                                                                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 4CLH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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    Val D:211 - Ala D:212   [ RasMol ]  
 

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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 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

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
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