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(-) Description

Title :  CRYSTAL STRUCTURES OF P DOMAIN OF NOROVIRUS VA387 IN COMPLEX WITH BLOOD GROUP TRISACCHARIDES TYPE B
 
Authors :  S. Cao, X. Li, Z. Rao
Date :  20 Dec 06  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Crystal Structures, P Domain, Norovirus Va387, Blood Group Trisaccharides Type B, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cao, Z. Lou, M. Tan, Y. Chen, Y. Liu, Z. Zhang, X. C. Zhang, X. Jiang, X. Li, Z. Rao
Structural Basis For The Recognition Of Blood Group Trisaccharides By Norovirus
J. Virol. V. 81 5949 2007
PubMed-ID: 17392366  |  Reference-DOI: 10.1128/JVI.00219-07
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN
    Mutation: YES
    Organism Scientific: NOROVIRUS
    Organism Taxid: 142786
    Strain: VA387

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GLA1Ligand/IonALPHA D-GALACTOSE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3GLA2Ligand/IonALPHA D-GALACTOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGAL A:2 , GLA A:3 , SER A:343 , THR A:344 , ARG A:345 , ASP A:374 , SER A:441 , GLY A:442BINDING SITE FOR RESIDUE FUC A 1
2AC2SOFTWAREFUC A:1 , GLA A:3 , ASP A:517 , SER A:518 , TRP A:519 , HOH A:645 , HOH A:763BINDING SITE FOR RESIDUE GAL A 2
3AC3SOFTWAREFUC A:1 , GAL A:2 , HIS A:347 , ASP A:374 , HOH A:699 , HOH A:724BINDING SITE FOR RESIDUE GLA A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OBT)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:398 -Pro A:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OBT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OBT)

(-) Exons   (0, 0)

(no "Exon" information available for 2OBT)

(-) 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:307
 aligned with Q913Z3_9CALI | Q913Z3 from UniProtKB/TrEMBL  Length:539

    Alignment length:307
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       
         Q913Z3_9CALI   224 TKPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICTFRGDVTHIAGSHDYIMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGMLTQTTREDGSTRAHKATVSTGSVHFTPKLGSVQYTTDTNNDLQTGQNTKFTPVGVIQDGNNHQNEPQQWVLPNYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGPHDLVIPPNGYFRFDSWVNQFYTLAPMG 530
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Calici_coat-2obtA01 A:224-291                                       -----------Calici_coat_C-2obtA02 A:303-530                                                                                                                                                                                                      Pfam domains
         Sec.struct. author .........hhhhh..........eeee..................................eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee...........eeeeee...........eeeeeeeee..................hhhhh...............eeeeeeeee..eee.....eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2obt A 224 TKPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICTFRGDVTHIAGSHDYIMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGMLTQTTREDGSTRAHKATVSTGSVHFTPKLGSVQYTTDTNNDLQTGQNTKFTPVGVIQDGNNHQNEPQQWVLPNYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGPHDLVIPPNGYFRFDSWVNQFYTLAPMG 530
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2OBT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OBT)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Calici_coat_C] (19)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2OBT)

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 Related Entries

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        Q913Z3_9CALI | Q913Z3: 2obr 2obs

(-) Related Entries Specified in the PDB File

2obr 2obs