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(-) Description

Title :  PRD1 VERTEX PROTEIN P5
 
Authors :  M. C. Merckel, J. T. Huiskonen, A. Goldman, D. H. Bamford, R. Tuma
Date :  01 Feb 05  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Beta-Spiral, Beta-Jelly-Roll, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Merckel, J. T. Huiskonen, D. H. Bamford, A. Goldman, R. Tuma
The Structure Of The Bacteriophage Prd1 Spike Sheds Light On The Evolution Of Viral Capsid Architecture.
Mol. Cell V. 18 161 2005
PubMed-ID: 15837420  |  Reference-DOI: 10.1016/J.MOLCEL.2005.03.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MINOR CAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 197-340
    Organism Scientific: ENTEROBACTERIA PHAGE PRD1
    Organism Taxid: 10658
    Synonym: PROTEIN P5

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1YQ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 1YQ6)

(-) 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
 aligned with P5_BPPRD | P22536 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:144
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336    
             P5_BPPRD   197 GGVTDALSLMYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITMTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVPSLDVLKFSLCNDGAALSNYIINITAAKIN 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.......................eeeeee...eee....eee.....eeeeeeeeee.......eeeeeeee..eeeeeeee......eeeeeeeeee.........eeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yq6 A 197 GGVTDALSLmYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITmTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVVSLDVLKFSLCNDGAALSNYIINITAAKIN 340
                                   206       216       226       236       246       256    |  266       276       286       296       306       316       326       336    
                                   206-MSE                                                261-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with P5_BPPRD | P22536 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:144
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336    
             P5_BPPRD   197 GGVTDALSLMYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITMTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVPSLDVLKFSLCNDGAALSNYIINITAAKIN 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.......................eeeeee...eee....eee.....eeeeeeeeee.......eeeeeeee..eeeeeeee......eeeeeeeeee.........eeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yq6 B 197 GGVTDALSLmYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITmTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVVSLDVLKFSLCNDGAALSNYIINITAAKIN 340
                                   206       216       226       236       246       256    |  266       276       286       296       306       316       326       336    
                                   206-MSE                                                261-MSE                                                                           


Chain C from PDB  Type:PROTEIN  Length:144
 aligned with P5_BPPRD | P22536 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:144
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336    
             P5_BPPRD   197 GGVTDALSLMYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITMTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVPSLDVLKFSLCNDGAALSNYIINITAAKIN 340
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DUF1860-1yq6C01 C:197-339                                                                                                                      - Pfam domains (1)
           Pfam domains (2) DUF1860-1yq6C02 C:197-339                                                                                                                      - Pfam domains (2)
           Pfam domains (3) DUF1860-1yq6C03 C:197-339                                                                                                                      - Pfam domains (3)
         Sec.struct. author ....eeeeeee.......................eeeeee...eee....eee.....eeeeeeeeee.......eeeeeeee..eeeeeeee......eeeeeeeeee.........eeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yq6 C 197 GGVTDALSLmYSTSTGGPASIAANALTDFDLSGALTVNSVGTGLTKSAAGIQLAAGKSGLYQITmTVKNNTVTTGNYLLRVKYGSSDFVVACPASSLTAGGTISLLIYCNVLGVVSLDVLKFSLCNDGAALSNYIINITAAKIN 340
                                   206       216       226       236       246       256    |  266       276       286       296       306       316       326       336    
                                   206-MSE                                                261-MSE
   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 1YQ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YQ6)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF1860] (2)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (P5_BPPRD | P22536)
cellular component
    GO:0098029    icosahedral viral capsid, spike    A short structure attached to an icosahedral virion capsid, and used for attachment to the host cell.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  1yq6
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 Related Entries

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

UniProtKB/Swiss-Prot
        P5_BPPRD | P22536: 1yq5 1yq8

(-) Related Entries Specified in the PDB File

1yq5 THE SAME PROTEIN, ANOTHER SPACE GROUP
1yq8 THE SAME PROTEIN, ANOTHER DOMAIN