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(-) Description

Title :  2E8 FAB FRAGMENT
 
Authors :  B. Rupp, S. Trakhanov
Date :  14 Mar 98  (Deposition) - 05 Aug 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  H,L,M,P
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  M,P  (1x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Trakhanov, S. Parkin, R. Raffai, R. Milne, Y. M. Newhouse, K. H. Weisgraber, B. Rupp
Structure Of A Monoclonal 2E8 Fab Antibody Fragment Specifi For The Low-Density Lipoprotein-Receptor Binding Region Of Apolipoprotein E Refined At 1. 9 A.
Acta Crystallogr. , Sect. D V. Null 122 1999
PubMed-ID: 10089402  |  Reference-DOI: 10.1107/S090744499800938X

(-) Compounds

Molecule 1 - IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
    Cell: LYMPHOCYTE-PLASMA CELL
    Cell Line: 2E8 HYBRIDOMA
    Chains: L, M
    Fragment: FAB FRAGMENT
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)
    Cell: LYMPHOCYTE-PLASMA CELL
    Cell Line: 2E8 HYBRIDOMA
    Chains: H, P
    Fragment: FAB FRAGMENT
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HLMP
Biological Unit 1 (1x): HL  
Biological Unit 2 (1x):   MP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 12E8)

(-) Sites  (0, 0)

(no "Site" information available for 12E8)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194
5M:23 -M:88
6M:134 -M:194
7P:22 -P:92
8P:140 -P:195

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Trp H:188 -Pro H:189
6Tyr M:94 -Pro M:95
7Tyr M:140 -Pro M:141
8Phe P:146 -Pro P:147
9Glu P:148 -Pro P:149
10Trp P:188 -Pro P:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 12E8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 12E8)

(-) Exons   (0, 0)

(no "Exon" information available for 12E8)

(-) 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 H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d12e8h1 H:1-114 Immunoglobulin heavy chain variable domain, VH                                                           d12e8h2 H:115-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 12e8H01 H:1-113 Immunoglobulins                                                                                         12e8H02 H:114-212 Immunoglobulins                                                                  -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee...hhheeeeeeee.....eeeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeeeee.............eeeeee.......eeeee...........eeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeee.hhh......eeeeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                12e8 H    1 EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52A                            82A||               100A||                                                                                                                  
                                                                                                              82B|                100B|                                                                                                                  
                                                                                                               82C                 100C                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d12e8l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d12e8l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 12e8L01 L:1-107 Immunoglobulins                                                                            12e8L02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                12e8 L    1 DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d12e8m1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d12e8m2 M:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 12e8M01 M:1-107 Immunoglobulins                                                                            12e8M02 M:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee........eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                12e8 M    1 DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain P from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains d12e8p1 P:1-114 Immunoglobulin heavy chain variable domain, VH                                                           d12e8p2 P:115-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 12e8P01 P:1-113 Immunoglobulins                                                                                         12e8P02 P:114-212 Immunoglobulins                                                                  -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....eeeeeeee...hhheeeeeeee.....eeeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeeeee.............eeeeee.......eeeee..........eeeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                12e8 P    1 EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEYVPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123       133       143       153       163       173       183       193       203       213 
                                                                              52A                            82A||               100A||                                                                                                                  
                                                                                                              82B|                100B|                                                                                                                  
                                                                                                               82C                 100C
   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  (4, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a12e8L02L:108-211
1b12e8H02H:114-212
1c12e8P02P:114-212
1d12e8M02M:108-211
1e12e8L01L:1-107
1f12e8M01M:1-107
1g12e8H01H:1-113
1h12e8P01P:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 12E8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 12E8)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu P:148 - Pro P:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe P:146 - Pro P:147   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Trp P:188 - Pro P:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
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    Tyr M:94 - Pro M:95   [ RasMol ]  
 
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  12e8
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