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(-) Description

Title :  CRYSTAL STRUCTURE OF TRICHINELLA SPIRALIS THYMIDYLATE SYNTHASE COMPLEXED WITH DUMP
 
Authors :  A. Dowiercial, A. Jarmula, W. Rypniewski, T. Fraczyk, P. Wilk, W. Rode
Date :  10 Jun 15  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Trichinella Spiralis, Parasitic Nematode, Protein-Ligand Complex, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dowiercial, P. Wilk, W. Rypniewski, T. Fraczyk, A. Jarmula, K. Banaszak, M. Dabrowska, J. Ciesla, W. Rode
Crystal Structures Of Thymidylate Synthase From Nematodes, Trichinella Spiralis And Caenorhabditis Elegans, As A Potential Template For Species-Specific Drug Design
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TX61-
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TS, TSP_03568
    Organism Common: TRICHINA WORM
    Organism Scientific: TRICHINELLA SPIRALIS
    Organism Taxid: 6334

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GOL8Ligand/IonGLYCEROL
3UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GOL4Ligand/IonGLYCEROL
3UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1DTT-1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GOL4Ligand/IonGLYCEROL
3UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:43 , CYS A:189 , HIS A:190 , GLN A:208 , ARG A:209 , SER A:210 , ALA A:211 , ASP A:212 , GLY A:216 , ASN A:220 , HIS A:250 , TYR A:252 , HOH A:559 , HOH A:616 , HOH A:640 , ARG B:169 , ARG B:170binding site for residue UMP A 401
02AC2SOFTWAREGLU A:81 , HOH A:616binding site for residue DTT A 402
03AC3SOFTWAREGLY A:137 , ASN A:177 , HOH A:524 , ASN B:177binding site for residue GOL A 403
04AC4SOFTWARECYS A:179 , GLY B:137 , GLY B:151binding site for residue GOL A 404
05AC5SOFTWAREASP A:257 , ILE A:275 , LEU A:276 , ARG A:277 , ASN A:278binding site for residue GOL A 405
06AC6SOFTWARETYR A:152 , ASP A:153 , GLN A:157 , HOH A:531 , ASN D:119binding site for residue GOL A 406
07AC7SOFTWAREARG A:169 , ARG A:170 , ARG B:43 , CYS B:189 , HIS B:190 , GLN B:208 , ARG B:209 , SER B:210 , ALA B:211 , ASP B:212 , ASN B:220 , HIS B:250 , TYR B:252 , HOH B:531 , HOH B:552binding site for residue UMP B 401
08AC8SOFTWAREARG C:43 , CYS C:189 , HIS C:190 , GLN C:208 , ARG C:209 , SER C:210 , ALA C:211 , ASP C:212 , GLY C:216 , ASN C:220 , HIS C:250 , TYR C:252 , HOH C:591 , HOH C:607 , HOH C:648 , HOH C:667 , ARG D:169 , ARG D:170binding site for residue UMP C 401
09AC9SOFTWARECYS C:179 , GLY D:137 , GLY D:151binding site for residue GOL C 402
10AD1SOFTWAREARG C:169 , ARG C:170 , ARG D:43 , CYS D:189 , HIS D:190 , GLN D:208 , ARG D:209 , SER D:210 , ALA D:211 , ASP D:212 , GLY D:216 , ASN D:220 , HIS D:250 , TYR D:252 , HOH D:591 , HOH D:599binding site for residue UMP D 401
11AD2SOFTWAREGLY D:151 , TYR D:152 , ASP D:153 , GLN D:157 , HOH D:524binding site for residue GOL D 402
12AD3SOFTWAREPHE C:136 , GLY C:151 , TYR C:152 , CYS D:179 , HOH D:553binding site for residue GOL D 403
13AD4SOFTWAREILE D:102 , ASN D:106 , HOH D:505 , HOH D:572binding site for residue GOL D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BY6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BY6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BY6)

(-) Exons   (0, 0)

(no "Exon" information available for 5BY6)

(-) Sequences/Alignments

Asymmetric 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhh....hhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhhhh.eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5by6 A  17 DYVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPLLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGLYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGVPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKPRPFPKLKILRNVENIDDFRAEDFELINYKPYPK 300
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5by6 B  17 DYVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPLLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGLYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGVPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKPRPFPKLKILRNVENIDDFRAEDFELINYKPYPKISMP 304
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296        


Chain C from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhh....hhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5by6 C  18 YVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPLLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGLYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGVPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKPRPFPKLKILRNVENIDDFRAEDFELINYKPYPKISM 303
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297      


Chain D from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhh........eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5by6 D  18 YVNQEELNYLNQLKDIIDHGVRKNDRTGIGTLSTFGTQSRYCLRDDIFPLLTTKRVFWRGVVEELLWFISGSTNAKQLSEKNVNIWDGNSSREFLDSRGLYNYEEGDLGPVYGFQWRHFGCPYSSMTADYKGKGYDQLQQCIKMIREEPESRRIIMTAWNPCDLEKVALPPCHCFVQFYVADGELSCQMYQRSADMGLGVPFNIASYSLLTRMIAHITSLKPGFFIHTIGDAHVYLTHVDALKVQMERKPRPFPKLKILRNVENIDDFRAEDFELINYKPYP 299
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   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 ; only for superseded entry 4G9U: 1,4)

(no "SCOP Domain" information available for 5BY6, only for superseded entry 4G9U replaced by 5BY6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BY6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BY6)

(-) Gene Ontology  (5, 5)

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