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(-) Description

Title :  FAB FRAGMENT OF MAB1-IA MONOCLONAL ANTIBODY TO HUMAN RHINOVIRUS 14 NIM-IA SITE
 
Authors :  Z. Che, T. J. Smith
Date :  03 Mar 98  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin, Neutralizes Human Rhinovirus, Igg1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Che, N. H. Olson, D. Leippe, W. M. Lee, A. G. Mosser, R. R. Rueckert, T. S. Baker, T. J. Smith
Antibody-Mediated Neutralization Of Human Rhinovirus 14 Explored By Means Of Cryoelectron Microscopy And X-Ray Crystallography Of Virus-Fab Complexes.
J. Virol. V. 72 4610 1998
PubMed-ID: 9573224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG1 FAB1-IA FAB (LIGHT CHAIN)
    Chains: A, C
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY
    Synonym: IGG1 IMMUNOGLOBULIN
 
Molecule 2 - IGG1 FAB1-IA FAB (HEAVY CHAIN)
    Chains: B, D
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY
    Synonym: IGG1 IMMUNOGLOBULIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1A6T)

(-) Sites  (0, 0)

(no "Site" information available for 1A6T)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:195
5C:23 -C:88
6C:134 -C:194
7D:22 -D:92
8D:140 -D:195

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2His A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A6T)

(-) Exons   (0, 0)

(no "Exon" information available for 1A6T)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains d1a6ta1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1a6ta2 A:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1a6tA01 A:1-108 Immunoglobulins                                                                            1a6tA02 A:109-210 Immunoglobulins                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeee.............eeeeee..eeeeee....hhh..eeeee.............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeeeeeee....eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a6t A   1 QSVLSQSPAILSASPGEKVIMTCSPSSSVSYMQWYQQKPGSSPKPWIYSTSNLASGVPGRFSGGGSGTSFSLTISGVEAEDAATYYCQQYSSHPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
                                                     27|                                                                                                                                                                                      
                                                      29                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1a6tb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d1a6tb2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1a6tB01 B:1-113 Immunoglobulins                                                                                      1a6tB02 B:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....eeee.hhh...eeeeeehhh.eeeeee....hhh.eeeeeeee....eeee...eeeee........eeeee............eeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeee...........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6t B   1 EVQLQQSGPDLVKPGASVKISCKASGYSFSTYYMHWVKQSHGKSLEWIGRVDPDNGGTSFNQKFKGKAILTVDKSSSTAYMELGSLTSEDSAVYYCARRDDYYFDFWGQGTSLTVSSAKTTPPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQTITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                                              52A                            82A||                                                                                                                                   
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d1a6tc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1a6tc2 C:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1a6tC01 C:1-108 Immunoglobulins                                                                            1a6tC02 C:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeee......eeee.............eeeeee..eeeeee....hhh..eeeee.............eeeee......eeeee...hhhh...eeeeeeeee......eeeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a6t C   1 QSVLSQSPAILSASPGEKVIMTCSPSSSVSYMQWYQQKPGSSPKPWIYSTSNLASGVPGRFSGGGSGTSFSLTISGVEAEDAATYYCQQYSSHPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
                                                     27|                                                                                                                                                                                      
                                                      29                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1a6td1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d1a6td2 D:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1a6tD01 D:1-113 Immunoglobulins                                                                                      1a6tD02 D:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeeee...........eeeee........eeeee............eeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeee...........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6t D   1 EVQLQQSGPDLVKPGASVKISCKASGYSFSTYYMHWVKQSHGKSLEWIGRVDPDNGGTSFNQKFKGKAILTVDKSSSTAYMELGSLTSEDSAVYYCARRDDYYFDFWGQGTSLTVSSAKTTPPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQTITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                                              52A                            82A||                                                                                                                                   
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C
   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)
1a1a6tC02C:109-211
1b1a6tB02B:114-212
1c1a6tD02D:114-212
1d1a6tB01B:1-113
1e1a6tD01D:1-113
1f1a6tA02A:109-210
1g1a6tA01A:1-108
1h1a6tC01C:1-108

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A6T)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1A6T)

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  Cis Peptide Bonds
    His A:94 - Pro A:95   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
 
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  1a6t
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