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(-) Description

Title :  TRYPANOSOMA BRUCEI PTR1 IN COMPLEX WITH INHIBITOR WH16
 
Authors :  E. Nerini, A. Dawson, W. N. Hunter, M. P. Costi
Date :  03 May 11  (Deposition) - 23 May 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Short Chain Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Nerini, A. Dawson, V. Hannaert, P. A. Michels, W. N. Hunter, M. P. Costi
Structural Studies Of Thiadiazole Derivatives That Inhibit Trypanosoma Brucei Growth.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE, PUTATIVE
    ChainsA, C
    EC Number1.5.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B_TBPTR1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET15BTEV
    Expression System Vector TypePLASMID
    Organism ScientificTRYPANOSOMA BRUCEI
    Organism Taxid5691
    Other DetailsCYS 59 OXIDIZED TO S-OXY CYSTEINE
    SynonymPTR1
 
Molecule 2 - PTERIDINE REDUCTASE, PUTATIVE
    ChainsB, D
    EC Number1.5.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B_TBPTR1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET15BTEV
    Organism ScientificTRYPANOSOMA BRUCEI
    Organism Taxid5691
    SynonymPTR1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CSX2Mod. Amino AcidS-OXY CYSTEINE
3DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5DTV1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
6NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
7W164Ligand/Ion5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:13 , ARG 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 , VAL A:206 , SER A:207 , LEU A:208 , W16 A:1270 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2011 , HOH A:2026 , HOH A:2064 , HOH A:2065 , HOH A:2155 , HOH A:2156BINDING SITE FOR RESIDUE NAP A1269
02AC2SOFTWAREPHE A:97 , ASP A:161 , TYR A:174 , MET A:213 , TRP A:221 , NAP A:1269 , DTV A:1271 , HOH A:2011 , HOH A:2065BINDING SITE FOR RESIDUE W16 A1270
03AC3SOFTWAREPHE A:97 , CYS A:168 , GLU A:217 , TRP A:221 , W16 A:1270 , ACT A:1272 , HOH A:2097BINDING SITE FOR RESIDUE DTV A1271
04AC4SOFTWAREPHE A:97 , DTV A:1271 , HOH A:2068BINDING SITE FOR RESIDUE ACT A1272
05AC5SOFTWAREARG 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 , LEU B:208 , W16 B:1270 , HOH B:2005 , HOH B:2006 , HOH B:2007 , HOH B:2009 , HOH B:2013 , HOH B:2025 , HOH B:2068 , HOH B:2069 , HOH B:2151BINDING SITE FOR RESIDUE NAP B1269
06AC6SOFTWAREPHE B:97 , ASP B:161 , TYR B:174 , TRP B:221 , NAP B:1269 , DTU B:1271 , HOH B:2069BINDING SITE FOR RESIDUE W16 B1270
07AC7SOFTWAREPHE B:97 , CYS B:168 , PHE B:171 , MET B:213 , TRP B:221 , W16 B:1270BINDING SITE FOR RESIDUE DTU B1271
08AC8SOFTWAREARG 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 , ASP C:161 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , VAL C:206 , SER C:207 , LEU C:208 , W16 C:1270 , HOH C:2002 , HOH C:2003 , HOH C:2004 , HOH C:2006 , HOH C:2018 , HOH C:2046 , HOH C:2048 , HOH C:2049 , HOH C:2100 , HOH C:2101BINDING SITE FOR RESIDUE NAP C1269
09AC9SOFTWAREPHE C:97 , ASP C:161 , TYR C:174 , TRP C:221 , NAP C:1269 , DTT C:1271 , HOH C:2048BINDING SITE FOR RESIDUE W16 C1270
10BC1SOFTWARECYS C:168 , MET C:213 , TRP C:221 , W16 C:1270BINDING SITE FOR RESIDUE DTT C1271
11BC2SOFTWARELYS D:13 , ARG 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 , ASP D:161 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , VAL D:206 , SER D:207 , LEU D:208 , W16 D:1270 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2008 , HOH D:2012 , HOH D:2028 , HOH D:2031 , HOH D:2072 , HOH D:2073 , HOH D:2124 , HOH D:2125BINDING SITE FOR RESIDUE NAP D1269
12BC3SOFTWAREPHE D:97 , ASP D:161 , TYR D:174 , MET D:213 , TRP D:221 , NAP D:1269 , DTT D:1271 , HOH D:2012 , HOH D:2073BINDING SITE FOR RESIDUE W16 D1270
13BC4SOFTWARECYS D:168 , MET D:213 , GLU D:217 , TRP D:221 , W16 D:1270 , ACT D:1272BINDING SITE FOR RESIDUE DTT D1271
14BC5SOFTWAREPHE D:97 , PRO D:99 , DTT D:1271BINDING SITE FOR RESIDUE ACT D1272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YHI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YHI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YHI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YHI)

(-) Exons   (0, 0)

(no "Exon" information available for 2YHI)

(-) 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:249
 aligned with Q581W1_TRYB2 | Q581W1 from UniProtKB/TrEMBL  Length:369

    Alignment length:267
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
         Q581W1_TRYB2   103 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 369
               SCOP domains d2yhia_ A: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee...........---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh---------...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yhi A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------SNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51       |61        71        81        91       101 |       - |     121       131       141|        -|      161       171       181       191       201       211       221       231       241       251       261       
                                                                                    59-CSX                                     103       113                          142       152                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q581W1_TRYB2 | Q581W1 from UniProtKB/TrEMBL  Length:369

    Alignment length:267
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
         Q581W1_TRYB2   103 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 369
               SCOP domains d2yhib_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee...........---------..hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yhi B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------SNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 |       - |     121       131       141|        -|      161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                               103       113                          142       152                                                                                                                    

Chain C from PDB  Type:PROTEIN  Length:249
 aligned with Q581W1_TRYB2 | Q581W1 from UniProtKB/TrEMBL  Length:369

    Alignment length:267
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
         Q581W1_TRYB2   103 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 369
               SCOP domains d2yhic_ C: automated matches                                                                                                                                                                                                                                                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
                 2yhi C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------SNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51       |61        71        81        91       101 |       - |     121       131       141|        -|      161       171       181       191       201       211       221       231       241       251       261       
                                                                                    59-CSX                                     103       113                          142       152                                                                                                                    

Chain D from PDB  Type:PROTEIN  Length:249
 aligned with Q581W1_TRYB2 | Q581W1 from UniProtKB/TrEMBL  Length:369

    Alignment length:267
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       
         Q581W1_TRYB2   103 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 369
               SCOP domains d2yhid_ D: automated matches                                                                                                                                                                                                                                                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
                 2yhi D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------SNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 |       - |     121       131       141|        -|      161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                               103       113                          142       152                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YHI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YHI)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q581W1_TRYB2 | Q581W1)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0047040    pteridine reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 H(+) + 2 NADPH.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q581W1_TRYB2 | Q581W13jq6 3jq7 3jq8 3jq9 3jqa 3jqb 3jqc 3jqd 3jqe 3jqf 3jqg

(-) Related Entries Specified in the PDB File

2x9g HIGH RESOLUTION STRUCTURE OF TBPTR1 IN COMPLEX WITH PEMETREXED