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(-) Description

Title :  CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH LEMON JUICE
 
Authors :  A. D. Koromyslova, G. S. Hansman
Date :  02 Jun 15  (Deposition) - 09 Sep 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Citrate, Lemon, Norovirus, Protruding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Koromyslova, P. A. White, G. S. Hansman
Treatment Of Norovirus Particles With Citrate.
Virology V. 485 199 2015
PubMed-ID: 26295280  |  Reference-DOI: 10.1016/J.VIROL.2015.07.009

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMBP
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: PROTRUDING DOMAIN, RESIDUES 224-538
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Strain: GII.10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FLC1Ligand/IonCITRATE ANION
3NO32Ligand/IonNITRATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:381 , HOH A:919 , HOH A:923 , THR B:534 , HOH B:749binding site for residue EDO A 601
2AC2SOFTWAREARG A:299 , THR A:380 , TRP A:381binding site for residue EDO A 602
3AC3SOFTWAREASN A:342 , ALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , SER A:387 , HOH A:702 , HOH A:722 , HOH A:786 , GLY B:451binding site for residue FLC A 603
4AC4SOFTWAREGLN A:471 , GLU B:464 , HIS B:468binding site for residue NO3 A 604
5AC5SOFTWAREASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:781 , HOH B:875 , HOH B:931binding site for residue EDO B 601
6AC6SOFTWAREPRO A:245 , LEU B:279 , THR B:281 , GLY B:282 , ARG B:287 , LYS B:393 , HOH B:835 , HOH B:886binding site for residue EDO B 602
7AC7SOFTWAREHIS B:302 , VAL B:361 , ALA B:363 , GLN B:377 , PHE B:378 , SER B:379 , HOH B:831binding site for residue NO3 B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BSY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BSY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BSY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BSY)

(-) Exons   (0, 0)

(no "Exon" information available for 5BSY)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               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
                 5bsy A 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294       304       314       324       334       344||     358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538
                                                                                                                                                  345|                                                                                                                                                                                            
                                                                                                                                                   350                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeeee.....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
                 5bsy B 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
   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 5BSY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BSY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BSY)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5BSY)

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  Cis Peptide Bonds
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  5bsy
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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 4z4y 4z4z 5bsx 5hza 5hzb

(-) Related Entries Specified in the PDB File

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