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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE 5'-METHYLTHIOADENOSINE/S-ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH METHYLTHIO-DADME-IMMUCILLIN-A
 
Authors :  S. A. Cameron, K. Thomas, S. C. Almo, V. L. Schramm
Date :  02 Oct 14  (Deposition) - 19 Aug 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Thomas, S. A. Cameron, S. C. Almo, E. S. Burgos, S. A. Gulab, V. L. Schramm
Active Site And Remote Contributions To Catalysis In Methylthioadenosine Nucleosidases.
Biochemistry V. 54 2520 2015
PubMed-ID: 25806409  |  Reference-DOI: 10.1021/BI501487W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE
    Chains: A, B
    EC Number: 3.2.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTNN, PFS, VC0395_A1957, VC395_2494
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1
    Organism Taxid: 345073
    Strain: ATCC 39541 / CLASSICAL OGAWA 395 / O395
    Synonym: MTAN,5'-METHYLTHIOADENOSINE NUCLEOSIDASE,MTA NUCLEOSIDASE,S- ADENOSYLHOMOCYSTEINE NUCLEOSIDASE,SRH NUCLEOSIDASE

 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
1TDI2Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:50 , SER A:76 , ALA A:77 , GLY A:78 , ALA A:151 , PHE A:152 , VAL A:153 , GLU A:173 , MET A:174 , GLU A:175 , SER A:197 , ASP A:198 , PHE A:208 , HOH A:485binding site for residue TDI A 301
2AC2SOFTWAREPHE A:105 , ILE B:50 , SER B:76 , ALA B:77 , GLY B:78 , ALA B:151 , PHE B:152 , VAL B:153 , GLU B:173 , MET B:174 , GLU B:175 , SER B:197 , ASP B:198 , PHE B:208 , HOH B:471binding site for residue TDI B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WKB)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhheeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhh.....eeeeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkb A   1 MKIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELLKENLYFQ 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhh.eeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhh.....eeeeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkb B   1 MKIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELLKENLYFQ 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
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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 4WKB)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (10, 10)

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        MTNN_VIBC3 | A5F5R2: 4x24

(-) Related Entries Specified in the PDB File

3dp9 3DP9 CONTAINS THE SAME PROTEIN COMPLEXED WITH BUTYLTHIO-DADME- IMMUCILLIN A