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(-) Description

Title :  FREE HSV-2 GD STRUCTURE
 
Authors :  G. Lu, N. Zhang, J. Qi, Y. Li, Z. Chen, C. Zheng, J. Yan, G. F. Gao
Date :  28 Sep 13  (Deposition) - 01 Oct 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Igv-Like Core, N-/C-Terminal Extensions, Receptor Binding, Nectin-1, Hvem, Viral Surface, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lu, N. Zhang, J. Qi, Y. Li, Z. Chen, C. Zheng, G. F. Gao, J. Yan
Crystal Structure Of Hsv-2 Gd Bound To Nectin-1 Reveals A Conserved Mode Of Receptor Recognition.
J. Virol. 2014
PubMed-ID: 25231300  |  Reference-DOI: 10.1128/JVI.01906-14

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN D
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell: HIGH5
    Expression System Cell Line: BTI-TN-5B1-4
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFAST-BAC1
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 26-310
    Gene: GD, US6
    Organism Common: HHV-2
    Organism Scientific: HUMAN HERPESVIRUS 2
    Organism Taxid: 10313
    Strain: 333
    Synonym: GD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:40 , GLN A:41 , ASN A:94 , HOH A:560 , HOH A:574 , HOH A:594 , HOH A:655BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWAREGLN B:41 , ASN B:94 , ASN B:171 , HOH B:590 , HOH B:638 , HOH B:705BINDING SITE FOR RESIDUE NAG B 401

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:106 -A:202
2A:118 -A:127
3B:106 -B:202
4B:118 -B:127

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:82 -Gly A:83
2Asp A:86 -Glu A:87
3Glu A:87 -Ala A:88
4Asp B:86 -Glu B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MYV)

(-) Sequences/Alignments

Asymmetric 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeee.......eee....hhhhhh..........eeeeeeeeeee....eeeeeeeeeeeee.........ee...ee.......ee......eee...hhhhheeeeeeeee..eeeeeeeeee.....hhhhh.hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myv A  37 VYHIQPSLEDPFQPPSIPITVYYAVLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPYNKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRLRIPPAACLTSKAYQQGVTVDSIGMLPR 222
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       196       206       216      
                                                                                                                                                                             184|                           
                                                                                                                                                                              195                           


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeee.....eeee....hhhhhh...........eeeeeeeeee....eeeeeeeeeeee..........ee...ee.......ee......eeee.......eeeeeeeee..eeeeeeeeeee....hhhhh.hhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myv B  37 VYHIQPSLEDPFQPPSIPITVYYAVLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPYNKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRLRIPPAACLTSKAYQQGVTVDSIGMLPR 222
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       196       206       216      
                                                                                                                                                                             184|                           
                                                                                                                                                                              195
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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 4MYV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:82 - Gly A:83   [ RasMol ]  
    Asp A:86 - Glu A:87   [ RasMol ]  
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    Glu A:87 - Ala A:88   [ RasMol ]  
 
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  4myv
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  GD_HHV23 | P03172
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 Related Entries

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

UniProtKB/Swiss-Prot
        GD_HHV23 | P03172: 4myw

(-) Related Entries Specified in the PDB File

1l2g FREE HSV-1 GD STRUCTURE
3u82 STRUCTURE OF HSV-1 GD BOUND TO NECTIN-1
4myw