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(-) Description

Title :  STRUCTURE OF PIN-DOMAIN PROTEIN (VAPC4 TOXIN) FROM PYROCOCCUS HORIKOSHII DETERMINED AT 2.2 A RESOLUTION
 
Authors :  A. Biswas, K. Hatti, N. Srinivasan, M. R. N. Murthy, K. Sekar
Date :  31 Oct 16  (Deposition) - 23 Nov 16  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrococcus Horikoshii, Hypothetical Protein, Pin-Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hatti, A. Biswas, S. Chaudhary, V. Dadireddy, K. Sekar, N. Srinivasan, M. R. N. Murthy
Structure Determination Of Contaminant Proteins Using The Marathonmr Procedure
J. Struct. Biol. V. 197 372 2017
PubMed-ID: 28167161  |  Reference-DOI: 10.1016/J.JSB.2017.01.005

(-) Compounds

Molecule 1 - RIBONUCLEASE VAPC4
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VAPC4, PH0500
    Organism Scientific: PYROCOCCUS HORIKOSHII OT3
    Organism Taxid: 70601
    Strain: OT3
    Synonym: PIN-DOMAIN PROTEIN

 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
1CD2Ligand/IonCADMIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:51 , LYS B:89 , GLU B:145binding site for residue CD A 201
2AC2SOFTWARELEU B:30 , ALA B:31 , PHE B:33binding site for residue CD B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H4H)

(-) Exons   (0, 0)

(no "Exon" information available for 5H4H)

(-) 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:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhh....hhhhhhhhhhhheee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h4h A   2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVE 145
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    


Chain B from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhh..hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..eeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h4h B   2 PLPPDITFDSLALIKMHSQNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKDIYNIVPLLDDIAIKAAQIEANLIKKEITLDMEDIITATTAIYTNSLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMVEK 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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 5H4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H4H)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  5h4h
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  VAPC4_PYRHO | O58236
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        VAPC4_PYRHO | O58236: 1v96 1ye5 5h4g

(-) Related Entries Specified in the PDB File

5h4g