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(-) Description

Title :  STRUCTURE OF THE SHIGELLA FLEXNERI VAPC MUTANT D7N
 
Authors :  K. Xu, E. Dedic, D. E. Brodersen
Date :  20 Oct 15  (Deposition) - 17 Feb 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  F (1x),J (1x)
Biol. Unit 2:  H (1x),L (1x)
Biol. Unit 3:  A,I  (1x)
Biol. Unit 4:  B,L  (1x)
Biol. Unit 5:  C,K  (1x)
Biol. Unit 6:  D  (2x)
Biol. Unit 7:  E (1x),H (1x)
Biol. Unit 8:  F (1x),J (1x)
Biol. Unit 9:  G  (2x)
Keywords :  Toxin, Pin-Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Xu, E. Dedic, D. E. Brodersen
Structural Analysis Of The Active Site Architecture Of The Vapc Toxin From Shigella Flexneri.
Proteins V. 84 892 2016
PubMed-ID: 26833558  |  Reference-DOI: 10.1002/PROT.25002

(-) Compounds

Molecule 1 - TRNA(FMET)-SPECIFIC ENDONUCLEASE VAPC
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    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

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x):      F (1x)   J (1x)  
Biological Unit 2 (1x):        H (1x)   L (1x)
Biological Unit 3 (1x): A       I   
Biological Unit 4 (1x):  B         L
Biological Unit 5 (1x):   C       K 
Biological Unit 6 (2x):    D        
Biological Unit 7 (1x):     E (1x)  H (1x)    
Biological Unit 8 (1x):      F (1x)   J (1x)  
Biological Unit 9 (2x):       G     

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5ED0)

(-) Sites  (0, 0)

(no "Site" information available for 5ED0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ED0)

(-) Cis Peptide Bonds  (19, 20)

Asymmetric Unit
No.Residues
1Lys A:18 -Pro A:19
2Lys B:18 -Pro B:19
3Lys C:18 -Pro C:19
4Asn C:116 -Thr C:117
5Thr C:117 -Arg C:118
6Lys D:18 -Pro D:19
7Lys E:18 -Pro E:19
8Asn E:116 -Thr E:117
9Lys F:18 -Pro F:19
10Gln F:90 -Gly F:91
11Thr F:117 -Arg F:118
12Lys G:18 -Pro G:19
13Lys H:18 -Pro H:19
14Lys I:18 -Pro I:19
15Lys J:18 -Pro J:19
16Ala J:20 -Ser J:21
17Gln J:90 -Gly J:91
18Lys K:18 -Pro K:19
19Lys L:18 -Pro L:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ED0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ED0)

(-) Exons   (0, 0)

(no "Exon" information available for 5ED0)

(-) 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: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
                 5ed0 A   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 B   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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..hhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 C   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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.......hhhhhhhhhh..eeee.hhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 D   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 E   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 F   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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...eeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 G   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 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..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..eeee.hhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 H   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain I 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..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 I   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain J from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh...hhhhhhhhh...eeeehhhhhhhhhhhhh..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..eeee.............eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 J   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain K from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeee.hhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 K   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain L 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..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ed0 L   1 HLKFMLNTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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  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 5ED0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ED0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ED0)

(-) Gene Ontology  (8, 8)

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    Asn C:116 - Thr C:117   [ RasMol ]  
    Asn E:116 - Thr E:117   [ RasMol ]  
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5ecd 5ECD CONTAINS THE SAME PROTEIN WITH A DIFFERENT MUTATION