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(-) Description

Title :  STRUCTURE OF THE SHIGELLA FLEXNERI VAPC MUTANT D98N CRYSTAL FORM 1
 
Authors :  K. Xu
Date :  20 Oct 15  (Deposition) - 17 Feb 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Toxin, Pin-Domain, Hepes, 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
    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

  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
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:9 , GLU A:42 , GLY A:95 , PRO A:96 , PHE A:97 , ASN A:98 , HOH A:310 , HOH A:405binding site for residue EPE A 201
2AC2SOFTWAREASN B:9 , GLU B:42 , GLY B:95 , PRO B:96 , PHE B:97 , ASN B:98 , HOH B:306binding site for residue EPE B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:18 -Pro A:19
2Lys B:18 -Pro B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ECD)

(-) 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...eeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecd 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..hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eee..hhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ecd B   1 HLKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTGQIRAELARQGRPVGPFNQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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)

(no "SCOP Domain" information available for 5ECD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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
        VAPC_SHIFL | O06662: 3tnd 5ecw 5ecy 5ed0

(-) Related Entries Specified in the PDB File

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