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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ANTI-HBV E-ANTIGEN MONOCLONAL FAB FRAGMENT (E6), UNBOUND
 
Authors :  M. A. Dimattia, N. R. Watts, S. J. Stahl, J. M. Grimes, A. C. Steven, D. I. S P. T. Wingfield
Date :  19 Dec 11  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  H,L  (1x)
Keywords :  Immunoglobulin Domain, Antibody Fab Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Dimattia, N. R. Watts, S. J. Stahl, J. M. Grimes, A. C. Steven, D. I. Stuart, P. T. Wingfield
Antigenic Switching Of Hepatitis B Virus By Alternative Dimerization Of The Capsid Protein.
Structure V. 21 133 2013
PubMed-ID: 23219881  |  Reference-DOI: 10.1016/J.STR.2012.10.017

(-) Compounds

Molecule 1 - FAB E6 HEAVY CHAIN
    Chains: A, C, E, H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB E6 LIGHT CHAIN
    Chains: B, D, F, L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHL
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3V6F)

(-) Sites  (0, 0)

(no "Site" information available for 3V6F)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:145 -A:200
3B:23 -B:94
4B:141 -B:201
5C:22 -C:92
6C:145 -C:200
7D:23 -D:94
8D:141 -D:201
9E:22 -E:92
10E:145 -E:200
11F:23 -F:94
12F:141 -F:201
13H:22 -H:92
14H:145 -H:200
15L:23 -L:94
16L:141 -L:201

(-) Cis Peptide Bonds  (23, 23)

Asymmetric Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Ser A:154
3Leu A:164 -Ser A:165
4Trp A:193 -Pro A:194
5Ser B:7 -Pro B:8
6Tyr B:147 -Pro B:148
7Gly C:100 -Ser C:101
8Phe C:151 -Pro C:152
9Glu C:153 -Ser C:154
10Trp C:193 -Pro C:194
11Ser D:7 -Pro D:8
12Tyr D:147 -Pro D:148
13Phe E:151 -Pro E:152
14Glu E:153 -Ser E:154
15Trp E:193 -Pro E:194
16Ser F:7 -Pro F:8
17Tyr F:147 -Pro F:148
18Gly H:100 -Ser H:101
19Phe H:151 -Pro H:152
20Glu H:153 -Ser H:154
21Trp H:193 -Pro H:194
22Ser L:7 -Pro L:8
23Tyr L:147 -Pro L:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V6F)

(-) Exons   (0, 0)

(no "Exon" information available for 3V6F)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeeeeeee.........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f A    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG  219
                                    10        20        30        40        50  |     59        69        79   |||  86        96      105H       115       125      |141       151       161       171       181       191       201       211        
                                                                              52A                            82A||                   105G|                        132|                                                                                
                                                                                                              82B|                    105H                         139                                                                                
                                                                                                               82C                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3v6fb1 B:1-114 automated matches                                                                                 d3v6fb2 B:115-219 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f B    1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain C from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeee..................eeeee........eeeee...eeeeeeeeeee.....eeee...eeeeeeeee..eeeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f C    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPSSVTLGCLVKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG  219
                                    10        20        30        40        50  |     59        69        79   |||  86        96      105H       115       125     ||142       152       167       177       187       197       207       217  
                                                                              52A                            82A||                   105G|                       131|                   161|                                                    
                                                                                                              82B|                    105H                        139                    167                                                    
                                                                                                               82C                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3v6fd1 D:1-114 automated matches                                                                                 d3v6fd2 D:115-219 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f D    1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain E from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeeeeee.......eeee...eeeee........eeeee...eeeeeeeeeee.....eeee..eeeeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f E    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPSSVTLGCLVKGYFPESVTVTWNSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG  219
                                    10        20        30        40        50  |     59        69        79   |||  86        96      105H       115       125     ||142       152       167       177       187       197       207       217  
                                                                              52A                            82A||                   105G|                       131|                  160|                                                     
                                                                                                              82B|                    105H                        139                   166                                                     
                                                                                                               82C                                                                                                                              


Chain F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3v6ff1 F:1-114 automated matches                                                                                 d3v6ff2 F:115-219 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f F    1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeee..................eeeee........eeeee...eeeeeeeeeee.....eeee.hhh.eeeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f H    1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGNYIYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTREGAYSGSSSYPMDYWGQGTSVTVSSAKTTPPSVYPLAPSSVTLGCLVKGYFPESVTVTWNSGSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG  219
                                    10        20        30        40        50  |     59        69        79   |||  86        96      105H       115       125     ||142       152       162||     174       184       194       204       214     
                                                                              52A                            82A||                   105G|                       131|                     163|                                                     
                                                                                                              82B|                    105H                        139                      166                                                     
                                                                                                               82C                                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d3v6fl1 L:1-114 automated matches                                                                                 d3v6fl2 L:115-219 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3v6f L    1 NIMMTQSPSSLAVSAGEKVTMNCKSSQSVLYSSNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQTEDLAVYYCHQYLSSYMYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V6F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V6F)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3V6F)

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  Cis Peptide Bonds
    Glu A:153 - Ser A:154   [ RasMol ]  
    Glu C:153 - Ser C:154   [ RasMol ]  
    Glu E:153 - Ser E:154   [ RasMol ]  
    Glu H:153 - Ser H:154   [ RasMol ]  
    Gly C:100 - Ser C:101   [ RasMol ]  
    Gly H:100 - Ser H:101   [ RasMol ]  
    Leu A:164 - Ser A:165   [ RasMol ]  
    Phe A:151 - Pro A:152   [ RasMol ]  
    Phe C:151 - Pro C:152   [ RasMol ]  
    Phe E:151 - Pro E:152   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Ser F:7 - Pro F:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp A:193 - Pro A:194   [ RasMol ]  
    Trp C:193 - Pro C:194   [ RasMol ]  
    Trp E:193 - Pro E:194   [ RasMol ]  
    Trp H:193 - Pro H:194   [ RasMol ]  
    Tyr B:147 - Pro B:148   [ RasMol ]  
    Tyr D:147 - Pro D:148   [ RasMol ]  
    Tyr F:147 - Pro F:148   [ RasMol ]  
    Tyr L:147 - Pro L:148   [ RasMol ]  
 
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  3v6f
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 Related Entries

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3v6z