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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDORABIES VIRUS GLYCOPROTEIN D
 
Authors :  A. Li, G. Lu, J. Qi, L. Wu, K. Tian, T. Luo, Y. Shi, J. Yan, G. F. Gao
Date :  17 Feb 17  (Deposition) - 26 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Herpes Simplex Virus, Pseudorabies Virus, Glycoprotein D, Viral Protein-Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Li, G. Lu, J. Qi, L. Wu, K. Tian, T. Luo, Y. Shi, J. Yan, G. F. Gao
Crystal Structure Of Pseudorabies Virus Glycoprotein D
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GD
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Gene: US6
    Organism Common: PSEUDORABIES VIRUS
    Organism Scientific: SUID HERPESVIRUS 1
    Organism Taxid: 10345
    Strain: BECKER
    Synonym: GLYCOPROTEIN D
 
Molecule 2 - NECTIN-1
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Fragment: UNP RESIDUES 37-143
    Gene: NECTIN1, HVEC, PRR1, PVRL1
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: HERPES VIRUS ENTRY MEDIATOR C,HVEC,NECTIN CELL ADHESION MOLECULE 1,POLIOVIRUS RECEPTOR-RELATED PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5X5W)

(-) Sites  (0, 0)

(no "Site" information available for 5X5W)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:66 -A:189
2A:105 -A:205
3A:117 -A:126
4B:15 -B:88
5C:66 -C:189
6C:105 -C:205
7C:117 -C:126
8D:15 -D:88

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Pro B:22 -Gly B:23
2Ala B:55 -Pro B:56
3Phe B:93 -Pro B:94
4Glu C:185 -Gly C:186
5Pro D:22 -Gly D:23
6Asn D:36 -Gly D:37
7Ala D:55 -Pro D:56
8Phe D:93 -Pro D:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X5W)

(-) Exons   (0, 0)

(no "Exon" information available for 5X5W)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee................eeee.........eeee.....hhhhhhhhhhh....eeeeeeeeee....eeeeeeeeeeee........eeeee..eehhhhhh.eee......eeee..hhhhheeeeeeeee..eeeeeeeee............hhhhhhhh...eehhhhhhhh.hhhhhhee..hhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x5w A  26 PTFPPPAYPYTESWQLTLTTVPSPFVGPADVYHTRPLEDPCGVVALISDPQVDRLLNEAVAHRRPTYRAHVAWYRIADGCAHLLYFIEYADCDPRQVFGRCRRRTTPMWWTPSADYMFPTEDELGLLMVAPGRFNEGQYRRLVSVDGVNILTDFMVALPEGQECPFARVDQHRTYKFGACWSDDSFKRGVDVMRFLTPFYQQPPHREVVNYWYRKNGRTLPRAYAAATPYAID 258
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeee...........eeeeeeeeeee..eeeeeeeee...eeee.......eee.........eeee..hhhhheeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5x5w B   1 DSMYGFIGTDVVLHCSFANPLPGVKITQVTWQKATNGSKQNVAIYNPAMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPAGNRESQLNLTVM 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain C from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee................eeee.........eeee.....hhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeee........eeeee..eehhhhhh.eee......eeee..hhhhheeeeeeeee..eeeeeeeee............hhhhhhhh...eehhhhhhhh.hhhhhhee..hhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x5w C  26 PTFPPPAYPYTESWQLTLTTVPSPFVGPADVYHTRPLEDPCGVVALISDPQVDRLLNEAVAHRRPTYRAHVAWYRIADGCAHLLYFIEYADCDPRQVFGRCRRRTTPMWWTPSADYMFPTEDELGLLMVAPGRFNEGQYRRLVSVDGVNILTDFMVALPEGQECPFARVDQHRTYKFGACWSDDSFKRGVDVMRFLTPFYQQPPHREVVNYWYRKNGRTLPRAYAAATPYAID 258
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   


Chain D from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeee.........eeeeeeeee.......eeeeee...eeee.......eee.......eeeee...hhhhheeeeeeeeee..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5x5w D   1 DSMYGFIGTDVVLHCSFANPLPGVKITQVTWQKATNGSKQNVAIYNPAMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPAGNRESQLNLTVM 107
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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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 5X5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X5W)

(-) Gene Ontology  (18, 20)

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  Cis Peptide Bonds
    Ala B:55 - Pro B:56   [ RasMol ]  
    Ala D:55 - Pro D:56   [ RasMol ]  
    Asn D:36 - Gly D:37   [ RasMol ]  
    Glu C:185 - Gly C:186   [ RasMol ]  
    Phe B:93 - Pro B:94   [ RasMol ]  
    Phe D:93 - Pro D:94   [ RasMol ]  
    Pro B:22 - Gly B:23   [ RasMol ]  
    Pro D:22 - Gly D:23   [ RasMol ]  
 
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