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(-) Description

Title :  NORWALK P DOMAIN A-TRISACCHARIDE COMPLEX
 
Authors :  R. Hegde, W. Bu
Date :  07 May 08  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norwalk P Domain A Trisaccaride Complex, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Bu, A. Mamedova, M. Tan, M. Xia, X. Jiang, R. S. Hegde
Structural Basis For The Receptor Binding Specificity Of Norwalk Virus.
J. Virol. V. 82 5340 2008
PubMed-ID: 18385236  |  Reference-DOI: 10.1128/JVI.00135-08
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 58 KD CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Fragment: UNP RESIDUES 230-530
    Organism Scientific: NORWALK VIRUS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NGA2Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:327 , HIS A:329 , SER A:377 , PRO A:378BINDING SITE FOR RESIDUE NGA A 531
2AC3SOFTWARESER A:380BINDING SITE FOR RESIDUE FUC A 533
3AC4SOFTWAREASP B:327 , HIS B:329 , TRP B:375 , SER B:377 , PRO B:378BINDING SITE FOR RESIDUE NGA B 531
4AC6SOFTWARESER B:380BINDING SITE FOR RESIDUE FUC B 533

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D26)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His B:381 -Pro B:382

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D26)

(-) Exons   (0, 0)

(no "Exon" information available for 3D26)

(-) 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:284
 aligned with CAPSD_NVN68 | Q83884 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:287
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       
          CAPSD_NVN68   230 PFTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.......eeeee.......hhhh.eee......eeeeeeeeeee....................-.--...............ee.eeeeee.....eeeee..hhhhhhhhhhh.......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d26 A 230 PFTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGS-I--ATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  |    409       419       429       439       449       459       469       479       489       499       509       
                                                                                                                                                                                                 397 |  |                                                                                                                  
                                                                                                                                                                                                   399  |                                                                                                                  
                                                                                                                                                                                                      402                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with CAPSD_NVN68 | Q83884 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:287
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       
          CAPSD_NVN68   230 PFTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.....-.eeeee.......hhhh.eee......eeeeeeeeeee.....-..............-..................ee.eeeeee.....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d26 B 230 PFTLPNLPLSSLSNSRAPLPISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHS-QTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHP-GSQVDLWKIPNYGS-ITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
                                   239       249       259       269       279       289       299       309       319       329        |-|      349       359       369       379  | |  389       399       409       419       429       439       449       459       469       479       489       499       509       
                                                                                                                                      338 |                                       382 |          397 |                                                                                                                     
                                                                                                                                        340                                         384            399
   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 3D26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D26)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CAPSD_NVN68 | Q83884)
cellular component
    GO:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a 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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  3d26
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 Related Entries

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

UniProtKB/Swiss-Prot
        CAPSD_NVN68 | Q83884: 1ihm 2zl5 2zl6 2zl7 3by1 3by2 5kw9 5n7m

(-) Related Entries Specified in the PDB File

1ihm CRYSTAL STRUCTURE ANALYSIS OF NORWALK VIRUS CAPSID
3by1 SAME PROTEIN, DIFFERENT CONSTRUCT
3by2 SAME PROTEIN, DIFFERENT CONSTRUCT