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(-) Description

Title :  CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 7.5MM B ANTIGEN (TRISACCHARIDE)
 
Authors :  M. M. Leuthold, A. D. Koromyslova, G. S. Hansman
Date :  02 Apr 15  (Deposition) - 27 May 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hbga, Norovirus, Protruding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Koromyslova, M. M. Leuthold, M. W. Bowler, G. S. Hansman
The Sweet Quartet: Binding Of Fucose To The Norovirus Capsid.
Virology V. 483 203 2015
PubMed-ID: 25980740  |  Reference-DOI: 10.1016/J.VIROL.2015.04.006

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMBP
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: PROTRUDING DOMAIN, UNP RESIDUES 224-538
    Organism Scientific: NOROVIRUS GII.10
    Organism Taxid: 747305

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
3GLA2Ligand/IonALPHA D-GALACTOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:279 , THR A:281 , GLY A:282 , ARG A:287 , HOH A:752 , HOH A:825 , PRO B:245binding site for residue EDO A 601
02AC2SOFTWAREARG A:299 , GLY A:300 , SER A:379 , THR A:380 , TRP A:381binding site for residue EDO A 602
03AC3SOFTWAREASN A:309 , LEU A:310 , ASN A:311 , LEU A:325 , HOH A:741 , HOH A:819 , HOH A:856binding site for residue EDO A 603
04AC4SOFTWAREPRO A:245 , ILE A:246 , HOH A:718 , HOH A:782 , HOH A:784 , ASN B:311 , HOH B:846binding site for residue EDO A 604
05AC5SOFTWAREPRO A:245 , LEU B:279 , THR B:281 , ALA B:285 , ARG B:287 , HOH B:780 , HOH B:846binding site for residue EDO B 601
06AC6SOFTWAREASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:745 , HOH B:812 , HOH B:821binding site for residue EDO B 602
07AC7SOFTWAREHIS A:358 , GLA A:607 , GLU B:359 , TRP B:381 , LYS B:449 , HOH B:731binding site for residue EDO B 603
08AC8SOFTWARESER B:379 , THR B:380 , TRP B:381binding site for residue EDO B 604
09AC9SOFTWAREGLY A:451 , TYR A:452 , ASN B:355 , HOH B:746 , HOH B:820binding site for residue EDO B 605
10AD1SOFTWAREALA A:354 , ASN A:355 , ARG A:356 , HIS A:358 , ASP A:385 , PHE A:532 , THR A:534 , HOH A:708 , HOH A:739 , HOH A:774 , HOH A:812 , HOH A:835 , HOH A:847 , HOH A:906 , GLY B:451 , TYR B:452 , EDO B:603binding site for Poly-Saccharide residues FUC A 605 through GLA A 607

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4Y)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeee......eeeeeee.........................eeeeeeeee....hhhhh...eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z4y A 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   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       533     


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeeee.....eeeeeee.........................eeeeeeeee....eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z4y B 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   233       243       253       263       273       283       293       303       313       323       333       343|      361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       
                                                                                                                                                 343|                                                                                                                                                                                          
                                                                                                                                                  352
   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 4Z4Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4Y)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Z4Y)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        Q5F4T5_9CALI | Q5F4T5: 3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3ry8 3v7a 4x7e 4x7f 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

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