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(-) Description

Title :  PROTRUDING DOMAIN OF GI.1 NOROVIRUS IN COMPLEX WITH 2-FUCOSYLLACTOSE (2FL)
 
Authors :  G. S. Hansman, A. D. Koromyslova
Date :  20 Feb 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Protruding Domain, Human Milk Oligosaccharides, 2Fl, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Koromyslova, S. Tripathi, V. Morozov, H. Schroten, G. S. Hansman
Human Norovirus Inhibition By A Human Milk Oligosaccharide.
Virology V. 508 81 2017
PubMed-ID: 28505592  |  Reference-DOI: 10.1016/J.VIROL.2017.04.032

(-) Compounds

Molecule 1 - CAPSID PROTEIN VP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMBP
    Expression System Taxid: 511693
    Gene: ORF2
    Organism Common: HU/NV/NV/1968/US
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 524364
    Other Details: SEQUENCE MAPS TO GENBANK ENTRY M87661.1, PROTEIN ID AAB50466.1, RESIDUES 224 TO 530
    Synonym: CP,P59

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLC2Ligand/IonALPHA-D-GLUCOSE
5NA2Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:352 , ASN A:394 , GLY A:396 , HOH A:821 , HOH A:898binding site for residue NA A 601
02AC2SOFTWARESER A:443 , HIS A:444 , SER A:447 , HOH A:892 , PRO B:234 , GLU B:440 , SER B:443 , HIS B:444 , EDO B:602binding site for residue EDO A 602
03AC3SOFTWAREASN A:235 , PRO A:464 , VAL A:502 , HOH A:735 , HOH A:809binding site for residue EDO A 603
04AC4SOFTWAREGLY A:278 , GLU A:313 , GLY A:314 , HIS A:404 , ALA A:406 , EDO A:606 , HOH A:729 , HOH A:746 , ARG B:275binding site for residue EDO A 604
05AC5SOFTWARELEU A:276 , EDO A:608 , HOH A:702binding site for residue EDO A 605
06AC6SOFTWAREVAL A:277 , GLY A:278 , ALA A:406 , EDO A:604 , HOH A:701 , HOH A:729binding site for residue EDO A 606
07AC7SOFTWARELYS A:424 , ALA A:430 , TYR A:431 , ASN A:432 , HOH A:703 , PHE B:335binding site for residue EDO A 607
08AC8SOFTWAREGLY A:274 , ARG A:275 , LEU A:276 , EDO A:605 , PHE B:312binding site for residue EDO A 608
09AC9SOFTWAREPHE B:352 , ASN B:394 , GLY B:396 , HOH B:818 , HOH B:894binding site for residue NA B 601
10AD1SOFTWAREPRO A:234 , LEU A:236 , GLU A:440 , SER A:443 , HIS A:444 , EDO A:602 , SER B:443 , HIS B:444 , SER B:447binding site for residue EDO B 602
11AD2SOFTWAREPRO B:464 , HOH B:707 , HOH B:737binding site for residue EDO B 603
12AD3SOFTWAREASP A:327 , HIS A:329 , GLN A:342 , ASP A:344 , TRP A:375 , SER A:377 , PRO A:378 , HOH A:709 , HOH A:718 , HOH A:737 , HOH A:744 , HOH A:799 , HOH A:855 , HOH A:881binding site for Poly-Saccharide residues GLC A 609 through FUC A 611
13AD4SOFTWARELEU A:276 , VAL A:277 , GLY A:278 , GLU A:313 , GLY A:314 , ASP A:327 , HIS A:329 , GLN A:342 , ASP A:344 , TRP A:375 , SER A:377 , PRO A:378 , HIS A:404 , ALA A:406 , EDO A:608 , GLC A:609 , HOH A:701 , HOH A:702 , HOH A:709 , HOH A:718 , HOH A:729 , HOH A:737 , HOH A:744 , HOH A:746 , HOH A:757 , HOH A:799 , HOH A:855 , ARG B:275 , ASP B:327 , HIS B:329 , GLN B:342 , ASP B:344 , TRP B:375 , SER B:377 , PRO B:378 , SER B:380 , HOH B:745 , HOH B:763 , HOH B:771 , HOH B:867binding site for Poly-Saccharide residues GLC B 604 through FUC B 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N7M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:381 -Pro A:382
2Asn A:486 -Gly A:487
3Thr A:518 -Ala A:519
4His B:381 -Pro B:382

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N7M)

(-) Exons   (0, 0)

(no "Exon" information available for 5N7M)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.......eeeee.......hhhh.eee......eeeeeeeeeee.......................................ee.eeeeee.....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee....hhhhh....eeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5n7m A 229 RPFTLPNLPLSSLSNSRAPLPISSIGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGGPQQLPINGVFVFVSWVSRFYQLKPVGTA 519
                                   238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       491       501       511        
                                                                                                                                                                                                                                                                                            487|                            
                                                                                                                                                                                                                                                                                             491                            


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eee............................hhhhh.eeeeee...eeee........hhhhh............eeeeeee.......eeeee.......hhhh.eee......eeeeeeeeeee.......................................eeeeeeeee.....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5n7m B 229 RPFTLPNLPLSSLSNSRAPLPISSIGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPV 516
                                   238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5N7M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N7M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N7M)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:486 - Gly A:487   [ RasMol ]  
    His A:381 - Pro A:382   [ RasMol ]  
    His B:381 - Pro B:382   [ RasMol ]  
    Thr A:518 - Ala A:519   [ RasMol ]  
 

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  CAPSD_NVN68 | Q83884
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        CAPSD_NVN68 | Q83884: 1ihm 2zl5 2zl6 2zl7 3by1 3by2 3d26 5kw9

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