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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IMMUNOGLOBULIN VARIABLE DOMAIN OF NECTIN-2 IN MONOCLINIC FORM
 
Authors :  U. A. Ramagopal, D. Samanta, S. G. Nathenson, S. C. Almo, New York Stru Genomics Research Consortium (Nysgrc), Atoms-To-Animals: The Function Network (Ifn)
Date :  14 Nov 12  (Deposition) - 30 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ig-Domain, Cell-Adhesion Molecule, Virus Entry Receptor, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  U. A. Ramagopal, D. Samanta, S. G. Nathenson, S. C. Almo
Crystal Structure Of The Immunoglobulin Variable Domain Of Nectin-2 In Monoclinic Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POLIOVIRUS RECEPTOR-RELATED PROTEIN 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentIG-LIKE V-TYPE DOMAIN RESIDUES 32-158
    GeneHVEB, PRR2, PVRL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHERPES VIRUS ENTRY MEDIATOR B, HERPESVIRUS ENTRY MEDIATOR B, HVEB, NECTIN-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4HZA)

(-) Sites  (0, 0)

(no "Site" information available for 4HZA)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:140
2B:54 -B:140

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:57 -Pro A:58
2Lys A:97 -Pro A:98
3Phe A:145 -Pro A:146
4Leu B:57 -Pro B:58
5Lys B:97 -Pro B:98
6Phe B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HZA)

(-) 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee......eee.eeee......eeeeeeee....hhhh.eeeeee...eee......hhh.eee...............eee...hhhhheeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hza A  31 MQDVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKMGPSFPSPKPGSERLSFVSAKQSTEAELQDATLALHGLTVEDEGNYTCEFATFPKGSVRGMTWLRV 158
                                    40        50        60        70        80        90       100       110||     124       134       144       154    
                                                                                                          111|                                          
                                                                                                           116                                          

Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eee......eee.eeee......eeeeeeee.........eeeeee...eee..........eee...............eee...hhhhheeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hza B  31 MQDVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKMGPSFPSPKPGSERLSFVSAKQSTEAELQDATLALHGLTVEDEGNYTCEFATFPKGSVRGMTWLRV 158
                                    40        50        60        70        80        90       100       110||     124       134       144       154    
                                                                                                          111|                                          
                                                                                                           116                                          

   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 4HZA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4hza)
 
  Cis Peptide Bonds
    Leu A:57 - Pro A:58   [ RasMol ]  
    Leu B:57 - Pro B:58   [ RasMol ]  
    Lys A:97 - Pro A:98   [ RasMol ]  
    Lys B:97 - Pro B:98   [ RasMol ]  
    Phe A:145 - Pro A:146   [ RasMol ]  
    Phe B:145 - Pro B:146   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        NECT2_HUMAN | Q926923r0n 4dfh 4dfi 5v52

(-) Related Entries Specified in the PDB File

3ron RELATED ID: NYSGRC-005598 RELATED DB: TARGETTRACK