Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT K13
 
Authors :  S. F. Harris, A. Villasenor, A. Kuglstatter
Date :  27 Aug 15  (Deposition) - 16 Dec 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,H
Biol. Unit 1:  A,H  (2x)
Keywords :  Helical Bundle, Antibody-Antigen Complex, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Bujotzek, F. Lipsmeier, S. F. Harris, J. Benz, A. Kuglstatter, G. Georges
Vh-Vl Orientation Prediction For Antibody Humanization Candidate Selection: A Case Study.
Mabs V. 8 288 2016
PubMed-ID: 26637054  |  Reference-DOI: 10.1080/19420862.2015.1117720

(-) Compounds

Molecule 1 - CD81 ANTIGEN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 112-201
    GeneCD81, TAPA1, TSPAN28
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym26 KDA CELL SURFACE PROTEIN TAPA-1,TARGET OF THE ANTIPROLIFERATIVE ANTIBODY 1,TETRASPANIN-28,TSPAN-28
 
Molecule 2 - SINGLE CHAIN FV FRAGMENT
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 101-810
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AH
Biological Unit 1 (2x)AH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5DFW)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:156 -A:190
2A:157 -A:175
3H:122 -H:330
4H:523 -H:734

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser H:507 -Pro H:508
2Thr H:796 -Pro H:797

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DFW)

(-) 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:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5dfw A 113 FVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPSGSNIISNLFKEDCHQKIDDLFSGKH 202
                                   122       132       142       152       162       172       182       192       202

Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...eee.....eeeeee....hhhh.eeeeeee.....eeeeeeee.....eee.hhhh...eeeee....eeeeee...hhhhheeeeeeee..........eeeee.....eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dfw H 102 VRLHQSAAQLVQPGASVRLSCTTSGFNFKDSYLHWVKQRPAQGLEWIGRIDTGNGNVKFDPKFQDKATITTDIPSMTAYLHLSNLTSEDTAVYYCVPYGYGFHSWGDGTTLTVSSDIQMTQSPASLSVSVGETVTITCRASENIYRTLAWYLQKQGKSPQLLVYGATTLADGVPSRFSGSGSGTQYYLKINSLQSEDFGTYHCQHFWGTPWTFGGGTKVEIK 810
                                   111       121   ||  156|  ||  206       252  ||   294    || 305       315       325      |353|  ||  406    || 505       515       552|||||| 601       611   ||| 698||     709  ||   721       731  ||   797 ||    808  
                                                 125|  156|  ||          214| 255|        299|                            332| ||  ||       411|                   523| |||||| 601           615||  699|        712|                734| 755|  ||         
                                                  151   196  ||           251  288         301                             351 ||  ||        501                    551 ||||||  |             651|   701         715                 751  796  ||         
                                                           199|                                                              353|  ||                                 553|||||  |              694                                           799|         
                                                            201                                                               396  ||                                  556||||  |                                                             801         
                                                                                                                                 399|                                   561|||  |                                                                         
                                                                                                                                  401                                    562||  |                                                                         
                                                                                                                                                                          571|  |                                                                         
                                                                                                                                                                           596  |                                                                         
                                                                                                                                                                              599                                                                         

   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 5DFW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5dfw)
 
  Sites
(no "Sites" information available for 5dfw)
 
  Cis Peptide Bonds
    Ser H:507 - Pro H:508   [ RasMol ]  
    Thr H:796 - Pro H:797   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dfw
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CD81_HUMAN | P60033
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CD81_HUMAN | P60033
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CD81_HUMAN | P600331g8q 1iv5 2avz 3x0e 5dfv 5m2c 5m33 5m3d 5m3t 5m4r 5tcx

(-) Related Entries Specified in the PDB File

5dfv