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(-) Description

Title :  CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 150MM 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
    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
1EDO7Ligand/Ion1,2-ETHANEDIOL
2FUL4Ligand/IonBETA-L-FUCOSE
3NO31Ligand/IonNITRATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:243 , PRO A:280 , THR A:281 , HOH A:716 , HOH A:749 , HOH A:834 , HOH A:850 , PRO B:243 , PRO B:280 , THR B:281binding site for residue EDO A 601
02AC2SOFTWARELEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325 , HOH A:704 , HOH A:724binding site for residue EDO A 602
03AC3SOFTWARETHR A:281 , HOH A:740 , HOH A:839 , HOH A:925 , PRO B:245binding site for residue EDO A 603
04AC4SOFTWAREARG A:299 , GLY A:300 , SER A:379 , THR A:380 , TRP A:381 , HOH A:736 , HOH A:879 , HOH A:922binding site for residue EDO A 604
05AC5SOFTWAREALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , PHE A:532 , HOH A:758 , HOH A:836 , HOH A:932 , GLY B:450 , GLY B:451 , TYR B:452binding site for residue FUL A 605
06AC6SOFTWAREGLU A:359 , TRP A:381 , LYS A:449 , HOH A:734 , HOH A:742 , HOH A:759 , HOH A:805 , HOH A:822 , HOH B:722binding site for residue FUL A 606
07AC7SOFTWAREGLY A:451 , TYR A:452 , HOH A:702 , HOH A:744 , VAL B:529 , ASN B:530 , TYR B:533 , FUL B:605binding site for residue NO3 A 607
08AC8SOFTWARESER B:379 , THR B:380 , TRP B:381 , HOH B:756binding site for residue EDO B 601
09AC9SOFTWAREASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:739 , HOH B:785 , HOH B:880binding site for residue EDO B 602
10AD1SOFTWAREPRO A:245 , LEU B:279 , THR B:281 , ARG B:287 , LYS B:393 , HOH B:730 , HOH B:820binding site for residue EDO B 603
11AD2SOFTWAREHOH A:773 , HOH A:822 , GLU B:359 , TRP B:381 , LYS B:449 , HOH B:741 , HOH B:746 , HOH B:762binding site for residue FUL B 604
12AD3SOFTWAREGLY A:450 , GLY A:451 , TYR A:452 , NO3 A:607 , HOH A:744 , ALA B:354 , ASN B:355 , ARG B:356 , ASP B:385 , ASN B:530 , HOH B:769 , HOH B:796binding site for residue FUL B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4S)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4S)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               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
                 4z4s A 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    


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.....eeeeeee.........................eeeeeeeee.........eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh..............................eeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z4s 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
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  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 4Z4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4S)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Z4S)

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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 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

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