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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) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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, 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  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2M2N4Ligand/Ion5,6-DIPHENYL-7H-PYRROLO[2,3-D]PYRIMIDINE-2,4-DIAMINE
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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 , VAL A:206 , SER A:207 , M2N A:1270 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2033 , HOH A:2038 , HOH A:2097 , HOH A:2100 , HOH A:2208 , HOH A:2209 , HOH A:2210BINDING SITE FOR RESIDUE NAP A 1269
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 , VAL B:206 , SER B:207 , M2N B:1270 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2033 , HOH B:2037 , HOH B:2101 , HOH B:2104 , HOH B:2189 , HOH B:2190BINDING SITE FOR RESIDUE NAP B 1269
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 , VAL C:206 , SER C:207 , M2N C:1270 , HOH C:2004 , HOH C:2005 , HOH C:2007 , HOH C:2011 , HOH C:2028 , HOH C:2072 , HOH C:2074 , HOH C:2147BINDING SITE FOR RESIDUE NAP C 1269
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 , M2N D:1270 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2012 , HOH D:2027 , HOH D:2028 , HOH D:2074 , HOH D:2086 , HOH D:2135 , HOH D:2137BINDING SITE FOR RESIDUE NAP D 1269
05AC5SOFTWAREARG A:14 , SER A:95 , PHE A:97 , ASP A:161 , MET A:163 , TYR A:174 , GLY A:205 , LEU A:209 , NAP A:1269 , HOH A:2210BINDING SITE FOR RESIDUE M2N A 1270
06AC6SOFTWARESER B:95 , PHE B:97 , ASP B:161 , TYR B:174 , GLY B:205 , VAL B:206 , LEU B:209 , NAP B:1269BINDING SITE FOR RESIDUE M2N B 1270
07AC7SOFTWAREARG C:14 , SER C:95 , PHE C:97 , ASP C:161 , TYR C:174 , GLY C:205 , VAL C:206 , LEU C:209 , NAP C:1269 , HOH C:2011BINDING SITE FOR RESIDUE M2N C 1270
08AC8SOFTWARESER D:95 , PHE D:97 , ASP D:161 , CYS D:168 , TYR D:174 , GLY D:205 , LEU D:209 , NAP D:1269 , HOH D:2012BINDING SITE FOR RESIDUE M2N D 1270
09AC9SOFTWAREGLN C:186 , GLY C:254 , ILE C:256 , HOH C:2137 , HOH C:2149 , HOH C:2150 , LYS D:258BINDING SITE FOR RESIDUE ACT C 1271
10BC1SOFTWAREGLN A:186 , GLY A:254 , ILE A:256 , HOH A:2196 , HOH A:2212 , HOH A:2213 , LYS B:258BINDING SITE FOR RESIDUE ACT A 1271
11BC2SOFTWARELYS A:258 , GLN B:186 , GLY B:254 , ILE B:256 , HOH B:2181BINDING SITE FOR RESIDUE ACT B 1271
12BC3SOFTWARELYS C:13 , ARG C:14 , ARG C:17 , HOH C:2009 , HOH C:2151BINDING SITE FOR RESIDUE ACT C 1272
13BC4SOFTWARECYS A:59 , GLN A:60 , SER A:72 , GLU A:75 , HOH A:2214 , SER D:53 , HOH D:2035 , HOH D:2041BINDING SITE FOR RESIDUE ACT A 1272
14BC5SOFTWARELYS C:258 , GLN D:186 , GLY D:254 , ILE D:256 , HOH D:2132 , HOH D:2138BINDING SITE FOR RESIDUE ACT D 1271

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CMA)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               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.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cma A   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                                                                                                                     


Chain B 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.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cma B   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                                                                                                                    


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


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...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cma 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4cm4 4cm5 4cm6 4cm7 4cm8 4cm9 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
4cm4 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
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