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(-) Description

Title :  CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 75MM FUCOSE
 
Authors :  A. D. Koromyslova, M. M. Leuthold, 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 :  Fucose, 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(DE3)
    Expression System Plasmid: PMBP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 224-538
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Synonym: GII.10 NOROVIRUS CAPSID PROTRUDING DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FUL4Ligand/IonBETA-L-FUCOSE
3NO31Ligand/IonNITRATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:299 , GLY A:300 , SER A:379 , THR A:380 , TRP A:381 , HOH A:784 , HOH A:846binding site for residue EDO A 601
02AC2SOFTWAREASN A:309 , LEU A:310 , ASN A:311 , LEU A:325 , HOH A:721 , HOH A:868 , HOH A:902binding site for residue EDO A 602
03AC3SOFTWAREGLU A:359 , TRP A:381 , LYS A:449 , HOH A:717 , HOH A:725 , HOH A:737 , HOH A:781 , HOH B:703binding site for residue FUL A 603
04AC4SOFTWAREALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , PHE A:532 , HOH A:734 , HOH A:903 , GLY B:450 , GLY B:451 , TYR B:452 , HOH B:817binding site for residue FUL A 604
05AC5SOFTWAREGLY A:451 , TYR A:452 , HOH A:702 , HOH A:711 , VAL B:529 , ASN B:530 , TYR B:533 , FUL B:606binding site for residue NO3 A 605
06AC6SOFTWAREASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:756 , HOH B:843 , HOH B:876binding site for residue EDO B 601
07AC7SOFTWAREPRO A:245 , LEU B:279 , THR B:281 , HOH B:802 , HOH B:835 , HOH B:912binding site for residue EDO B 602
08AC8SOFTWAREPRO A:243 , PRO A:280 , THR A:281 , PRO B:280 , THR B:281 , HOH B:798 , HOH B:821binding site for residue EDO B 603
09AC9SOFTWARESER B:379 , THR B:380 , TRP B:381 , HOH B:768 , HOH B:933binding site for residue EDO B 604
10AD1SOFTWAREHOH A:703 , HOH A:717 , GLU B:359 , TRP B:381 , LYS B:449 , HOH B:758 , HOH B:771 , HOH B:783binding site for residue FUL B 605
11AD2SOFTWAREGLY A:450 , GLY A:451 , NO3 A:605 , HOH A:702 , ALA B:354 , ASN B:355 , ARG B:356 , ASP B:385 , ASN B:530 , HOH B:743binding site for residue FUL B 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4T)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4T)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeee......eeeeeee.........................eeeeeeeee.........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
                 4z4t A 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294       304       314       324       334       344 ||    357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 
                                                                                                                                                   346|                                                                                                                                                                                            
                                                                                                                                                    350                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeeee.....eeeeeeee........................eeeeeeeee.........eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z4t B 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   233       243       253       263       273       283       293       303       313       323       333       343 ||    356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536  
                                                                                                                                                   345|                                                                                                                                                                                             
                                                                                                                                                    349
   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 4Z4T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4T)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Z4T)

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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 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Z4T)