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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH MURINE FAB FRAGMENT K04
 
Authors :  S. F. Harris, A. Wong, A. Kuglstatter
Date :  27 Aug 15  (Deposition) - 16 Dec 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Helical Bundle, Cell Adhesion, Antibody-Antigen Complex, Immune System (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, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    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 - FAB HEAVY CHAIN
    Cell LineMURINE HYBRIDOMA
    ChainsC, E
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - FAB LIGHT CHAIN
    Cell LineMURINE HYBRIDOMA
    ChainsD, F
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5DFV)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:156 -A:190
2A:157 -A:175
3B:156 -B:190
4B:157 -B:175
5C:122 -C:330
6C:1026 -C:1081
7D:523 -D:734
8D:2026 -D:2086
9E:122 -E:330
10E:1026 -E:1081
11F:523 -F:734
12F:2026 -F:2086

(-) Cis Peptide Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1Ser A:183 -Asn A:184
2Phe C:1032 -Pro C:1033
3Glu C:1034 -Pro C:1035
4Trp C:1074 -Pro C:1075
5Ser D:507 -Pro D:508
6Gly D:516 -Gln D:517
7His D:722 -Pro D:723
8Phe D:796 -Pro D:797
9Tyr D:2032 -Pro D:2033
10Phe E:1032 -Pro E:1033
11Glu E:1034 -Pro E:1035
12Thr E:1070 -Ser E:1071
13Ser E:1071 -Asn E:1072
14Trp E:1074 -Pro E:1075
15Ser F:507 -Pro F:508
16His F:722 -Pro F:723
17Phe F:796 -Pro F:797
18Tyr F:2032 -Pro F:2033

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DFV)

(-) 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:88
                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                5dfv A  113 FVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPSNIISNLFKEDCHQKIDDLFSGKH  202
                                   122       132       142       152       162       172    || 184       194        
                                                                                          177|                      
                                                                                           180                      

Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                5dfv B  113 FVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPSISNLFKEDCHQKIDDLFSGKH  202
                                   122       132       142       152       162       172    || 186       196      
                                                                                          177|                    
                                                                                           182                    

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee......eeeeeeeee.....eeee.hhh....eee...ee....eeeeeeee...........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dfv C  101 QVQLQQSGPELVKPGASVKISCKASGYTFSSSWMNWVKQRPGKGLEWIGRIYSGDGDAIYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREGKTGDLLLRSWGQGSALTVSSAKTTAPSVYPLVPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPR 1099
                                   110       120    || 155||  || 205       251   ||  293     ||304       314       324       352  ||   401       411|     1009   || 1025      1035      1045      1055      1065      1075      1085      1095    
                                                  125|  156|  ||          214| 255|        299|                            332| 355|  399|       411|         1013|                                                                               
                                                   151   196  ||           251  288         301                             351  394   401       1000          1020                                                                               
                                                            199|                                                                                                                                                                                  
                                                             201                                                                                                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee........eee...........eeeeeeeeehhhhhh....eeeeee..........ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dfv D  501 DIVLTQSPASLSVSLGQRATISCRASKSVSTSIYSYMHWYQQKPGQPPKLLIKYASYLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCEHSREFPFTFGTGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 2105
                                   510       520  || ||563|||    602       612  |||  699|      710 ||    722       732 ||   |798||     809||    2008      2018      2028      2038      2048      2058      2068      2078      2088      2098       
                                                523| ||| ||||  599|           615||  699|        712|                734| 755|  ||      810|                                                                                                         
                                                 551 ||| ||||   601            651|   701         715                 751  796  ||      2000                                                                                                         
                                                   553|| ||||                   694                                           799|                                                                                                                   
                                                    556| ||||                                                                  801                                                                                                                   
                                                     561 ||||                                                                                                                                                                                        
                                                       563|||                                                                                                                                                                                        
                                                        581||                                                                                                                                                                                        
                                                         582|                                                                                                                                                                                        
                                                          594                                                                                                                                                                                        

Chain E from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhh.eeeeeee......eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee.....eeeeeeeeee.....eeee........eee...eee..eeeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dfv E  101 QVQLQQSGPELVKPGASVKISCKASGYTFSSSWMNWVKQRPGKGLEWIGRIYSGDGDAIYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREGKTGDLLLRSWGQGSALTVSSAKTTAPSVYPLVPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPR 1099
                                   110       120    || 155||  || 205       251   ||  293     ||304       314       324       352  ||   401       411|     1009   || 1025      1035      1045      1055      1065      1075      1085      1095    
                                                  125|  156|  ||          214| 255|        299|                            332| 355|  399|       411|         1013|                                                                               
                                                   151   196  ||           251  288         301                             351  394   401       1000          1020                                                                               
                                                            199|                                                                                                                                                                                  
                                                             201                                                                                                                                                                                  

Chain F from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee........eee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dfv F  501 DIVLTQSPASLSVSLGQRATISCRASKSVSTSIYSYMHWYQQKPGQPPKLLIKYASYLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCEHSREFPFTFGTGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 2105
                                   510       520  || ||563|||    602       612  |||  699|      710 ||    722       732 ||   |798||     809||    2008      2018      2028      2038      2048      2058      2068      2078      2088      2098       
                                                523| ||| ||||  599|           615||  699|        712|                734| 755|  ||      810|                                                                                                         
                                                 551 ||| ||||   601            651|   701         715                 751  796  ||      2000                                                                                                         
                                                   553|| ||||                   694                                           799|                                                                                                                   
                                                    556| ||||                                                                  801                                                                                                                   
                                                     561 ||||                                                                                                                                                                                        
                                                       563|||                                                                                                                                                                                        
                                                        581||                                                                                                                                                                                        
                                                         582|                                                                                                                                                                                        
                                                          594                                                                                                                                                                                        

   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 5DFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Glu C:1034 - Pro C:1035   [ RasMol ]  
    Glu E:1034 - Pro E:1035   [ RasMol ]  
    Gly D:516 - Gln D:517   [ RasMol ]  
    His D:722 - Pro D:723   [ RasMol ]  
    His F:722 - Pro F:723   [ RasMol ]  
    Phe C:1032 - Pro C:1033   [ RasMol ]  
    Phe D:796 - Pro D:797   [ RasMol ]  
    Phe E:1032 - Pro E:1033   [ RasMol ]  
    Phe F:796 - Pro F:797   [ RasMol ]  
    Ser A:183 - Asn A:184   [ RasMol ]  
    Ser D:507 - Pro D:508   [ RasMol ]  
    Ser E:1071 - Asn E:1072   [ RasMol ]  
    Ser F:507 - Pro F:508   [ RasMol ]  
    Thr E:1070 - Ser E:1071   [ RasMol ]  
    Trp C:1074 - Pro C:1075   [ RasMol ]  
    Trp E:1074 - Pro E:1075   [ RasMol ]  
    Tyr D:2032 - Pro D:2033   [ RasMol ]  
    Tyr F:2032 - Pro F:2033   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DFV)