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(-) Description

Title :  STRUCTURE OF THE SHIGELLA FLEXNERI VAPC MUTANT D98N CRYSTAL FORM 2
 
Authors :  K. Xu, E. Dedic, D. E. Brodersen
Date :  20 Oct 15  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Toxin, Pin-Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xu, E. Dedic, D. E. Brodersen
Structural Analysis On The Active Site Architecture Of An Activated Vapc Toxin From Shigella Flexneri
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA(FMET)-SPECIFIC ENDONUCLEASE VAPC
    Chains: A, B, C, D, E, F, G, H
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: VAPC, MVPA, STBORF2, CP0245
    Mutation: YES
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Synonym: RNASE VAPC,TOXIN VAPC

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5ECY)

(-) Sites  (0, 0)

(no "Site" information available for 5ECY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Lys A:18 -Pro A:19
2Lys B:18 -Pro B:19
3Lys C:18 -Pro C:19
4Lys D:18 -Pro D:19
5Lys E:18 -Pro E:19
6Lys F:18 -Pro F:19
7Lys G:18 -Pro G:19
8Lys H:18 -Pro H:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ECY)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy A   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy B   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain C from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy C   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain D from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy D   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy E   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain F from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy F   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain G from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy G   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain H from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecy H   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 5ECY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 5ecy)
 
  Cis Peptide Bonds
    Lys A:18 - Pro A:19   [ RasMol ]  
    Lys B:18 - Pro B:19   [ RasMol ]  
    Lys C:18 - Pro C:19   [ RasMol ]  
    Lys D:18 - Pro D:19   [ RasMol ]  
    Lys E:18 - Pro E:19   [ RasMol ]  
    Lys F:18 - Pro F:19   [ RasMol ]  
    Lys G:18 - Pro G:19   [ RasMol ]  
    Lys H:18 - Pro H:19   [ RasMol ]  
 

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  5ecy
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  VAPC_SHIFL | O06662
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        VAPC_SHIFL | O06662: 3tnd 5ecd 5ecw 5ed0

(-) Related Entries Specified in the PDB File

5ecd 5ECD CONTAINS THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM