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(-) Description

Title :  CRYSTAL STRUCTURE OF C.ELEGANS THYMIDYLATE SYNTHASE IN COMPLEX WITH AN INHIBITOR N(4)OHDCMP
 
Authors :  P. Wilk, A. Jarmula, W. Rode
Date :  07 Mar 14  (Deposition) - 18 Feb 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Methyltransferase, Nucleotide Biosynthesis, Protein Dimer, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dowiercia, P. Wilk, W. Rypniewski, W. Rode, A. Jarmua
Crystal Structure Of C. Elegans Thymidylate Synthase In Complex With An Inhibitor N(4)Ohdcmp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPIGDM4+STOP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: ROUNDWORM
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NOH2Ligand/Ion2'-DEOXY-N-HYDROXYCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:197 , HIS A:198 , GLN A:216 , ARG A:217 , SER A:218 , GLY A:219 , ASP A:220 , GLY A:224 , ASN A:228 , HIS A:258 , TYR A:260 , ARG B:177 , ARG B:178 , HOH B:501BINDING SITE FOR RESIDUE NOH A 401
2AC2SOFTWAREARG A:177 , ARG A:178 , HOH A:502 , CYS B:197 , GLN B:216 , ARG B:217 , SER B:218 , GLY B:219 , ASP B:220 , GLY B:224 , ASN B:228 , HIS B:258 , TYR B:260BINDING SITE FOR RESIDUE NOH B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PSG)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee...............eeeeeeee...eeeeeeee..ee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee..........hhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psg A  24 QVHLNQDEYKYLKQVEQILREGTRRDDRTGTGTISIFGMQSKYCLRNGTIPLLTTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNLGFTSREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQPDSRRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGLGVPFNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDREPYAFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIPMD 312
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         


Chain B from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhhh..hhhhhhhh.........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh.....eeee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee..........hhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psg B  24 QVHLNQDEYKYLKQVEQILREGTRRDDRTGTGTISIFGMQSKYCLRNGTIPLLTTKRVYWKGVLEELLWFISGSTDGKLLMEKNVKIWEKNGDRAFLDNLGFTSREEGDLGPVYGFQWRHFGAKYVDCHTDYSGQGVDQLAEVIRQIKEQPDSRRIIMSAWNPSDLGQMVLPPCHTMCQFYVDNGELSCQLYQRSGDMGLGVPFNLASYGLLTHMIAKVCGLKPGTLVHTLGDAHVYSNHVDALKIQLDREPYAFPKIRFTRDVASIDDFTSDMIALDDYKCHPKIPMD 312
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303
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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 4PSG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Y052_CAEEL | Q9Y052: 5noo
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        Q9Y052_CAEEL | Q9Y052: 4iqb 4iqq 4irr 4isw

(-) Related Entries Specified in the PDB File

4ein 4ez8 4g9u 4iqb 4iqq 4irr