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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI N5, N10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE-CYCLOHYDROLASE (FOLD) COMPLEXED WITH NADP COFACTOR AND INHIBITOR
 
Authors :  T. C. Eadsforth, W. N. Hunter
Date :  23 Dec 13  (Deposition) - 04 Feb 15  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Eadsforth, A. Pinto, R. Luciani, L. Tamborini, G. Cullia, C. De Micheli, L. Marinelli, S. Cosconati, E. Novellino, L. Lo Presti, A. Cordeiro Da Silva, P. Conti, W. N. Hunter, M. P. Costi
Characterization Of 2, 4-Diamino-6-Oxo-1, 6-Dihydropyrimidin- 5-Yl Ureido Based Inhibitors Of Trypanosoma Brucei Fold And Testing For Antiparasitic Activity.
J. Med. Chem. V. 58 7938 2015
PubMed-ID: 26322631  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00687

(-) Compounds

Molecule 1 - C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC, PUTATIVE
    Chains: A, B
    EC Number: 1.5.1.5
    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 STRAIN 927/4 GUTAT10.1
    Organism Taxid: 999953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
19L92Ligand/Ion(2S)-2-[[4-[[2,4-BIS(AZANYL)-6-OXIDANYLIDENE-1H-PYRIMIDIN-5-YL]CARBAMOYLAMINO]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID
2GOL1Ligand/IonGLYCEROL
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:259 , HOH A:2171 , LYS B:246 , ARG B:251BINDING SITE FOR RESIDUE GOL A1298
2AC2SOFTWAREVAL A:110 , SER A:114 , LEU A:125 , ASP A:173 , HOH A:2177 , HIS B:134 , ILE B:135BINDING SITE FOR RESIDUE PEG A1299
3AC3SOFTWARETYR A:52 , LEU A:55 , LYS A:56 , VAL A:99 , GLN A:100 , LEU A:101 , ASP A:123 , ILE A:174 , PRO A:272 , GLY A:273 , GLY A:276 , PRO A:277 , NAP A:1301 , HOH A:2042 , HOH A:2046 , HOH A:2102 , HOH A:2173 , HOH A:2178 , HOH A:2179BINDING SITE FOR RESIDUE 9L9 A1300
4AC4SOFTWAREARG B:10 , TYR B:52 , LEU B:55 , LYS B:56 , VAL B:99 , GLN B:100 , LEU B:101 , ASP B:123 , ILE B:174 , LEU B:252 , PRO B:272 , GLY B:273 , GLY B:276 , PRO B:277 , HOH B:2031 , HOH B:2068 , HOH B:2069 , HOH B:2137 , HOH B:2139 , HOH B:2140 , HOH B:2141BINDING SITE FOR RESIDUE 9L9 B1298
5AC5SOFTWAREASP A:48 , TYR A:52 , PRO A:102 , GLY A:170 , ARG A:171 , GLY A:172 , ILE A:174 , ALA A:175 , HIS A:194 , SER A:195 , ALA A:215 , ALA A:216 , GLY A:217 , GLN A:218 , VAL A:236 , GLY A:237 , THR A:238 , 9L9 A:1300 , HOH A:2040 , HOH A:2142 , HOH A:2180 , ARG B:30BINDING SITE FOR RESIDUE NAP A1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:101 -Pro A:102
2Val A:271 -Pro A:272
3Leu B:101 -Pro B:102
4Val B:271 -Pro B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CJX)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhh..hhhh.....hhhhhh............hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeee........hhhhh....eeee...eeee.......eeee...hhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjx A   1 MPEAVVIDGRAVAKAIQKELTEEVALLERRYKGRRPGLSTIICGKRKDSQTYVRLKRKAAAACGFRNFSVELPANVTQEALEREVIRLNEEEACHSIVVQLPLPPHIDKVAALSKIKPEKDADCLLPVNVGQLHIRERNPAIVPCTASAVMELLRCSGVEICGKRVVVLGRGDIAGLPVATLLANEDATVTVVHSATPLCDIADIVRASDIVVSAAGQPGLVRGEWIKLGAAVIDVGTTPVADPSKVPGYRLVGDVCFDVARKRAAYITPVPGGVGPVTVSMLLKNTLTMFKRSVRA 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       


Chain B from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh.....eeee........hhhhhhh..hhhh.....hhhhhh............hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeee........hhhhh....eeee...eeee.......eeee...hhhhhh....ee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cjx B   1 MPEAVVIDGRAVAKAIQKELTEEVALLERRYKGRRPGLSTIICGKRKDSQTYVRLKRKAAAACGFRNFSVELPANVTQEALEREVIRLNEEEACHSIVVQLPLPPHIDKVAALSKIKPEKDADCLLPVNVGQLHIRERNPAIVPCTASAVMELLRCSGVEICGKRVVVLGRGDIAGLPVATLLANEDATVTVVHSATPLCDIADIVRASDIVVSAAGQPGLVRGEWIKLGAAVIDVGTTPVADPSKVPGYRLVGDVCFDVARKRAAYITPVPGGVGPVTVSMLLKNTLTMFKRSVRA 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:101 - Pro A:102   [ RasMol ]  
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    Val B:271 - Pro B:272   [ RasMol ]  
 

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