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(-) Description

Title :  ANTIGEN-BINDING FRAGMENT OF THE MURINE ANTI-PHENYLARSONATE ANTIBODY 36-71, "FAB 36-71"
 
Authors :  B. Parhami-Seren, M. Viswanathan, R. K. Strong, M. N. Margolies
Date :  21 Jun 01  (Deposition) - 27 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Parhami-Seren, M. Viswanathan, R. K. Strong, M. N. Margolies
Structural Analysis Of Mutants Of High-Affinity And Low-Affinity P-Azophenylarsonate-Specific Antibodies Generated By Alanine Scanning Of Heavy Chain Complementarity-Determining Region 2.
J. Immunol. V. 167 5129 2001
PubMed-ID: 11673524
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA CELLS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JFQ)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:322 -H:396
2H:448 -H:503
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:454 -Pro H:455
4Glu H:456 -Pro H:457
5Arg H:496 -Pro H:497

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JFQ)

(-) 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 H from PDB  Type:PROTEIN  Length:220
 aligned with HVM03_MOUSE | P01747 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:220
                                                                                                                                                 120                                                                                                    
                                    10        20        30        40        50        60        70        80        90       100       110       120         -         -         -         -         -         -         -         -         -         -
          HVM03_MOUSE     1 VQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVSS----------------------------------------------------------------------------------------------------   -
               SCOP domains d1jfqh1 H:302-421 Immunoglobulin heavy chain variable domain, VH                                                        d1jfqh2 H:422-521 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1jfqH01 H:302-421 Immunoglobulins                                                                                       1jfqH02 H:422-521 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfq H 302 VQLQQSGVELVRAGSSVKMSCKASGYTFTSNGINWVKQRPGQGLEWIGYNNPGNGYITYNEKFKGKTTLTVDKSSNTAYMQLRSLTSEDSAVYFCARSEYYGGSYKFDYWGQGTTLTVSSAGTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR 521
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521


Chain L from PDB  Type:PROTEIN  Length:215
 aligned with KV5AF_MOUSE | P01648 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:215
                                                                                                                                     108                                                                                                           
                                    10        20        30        40        50        60        70        80        90       100       | -         -         -         -         -         -         -         -         -         -         -     
          KV5AF_MOUSE     1 DIQMTQTPSSLSASLGDRVTISCRASQDINNYLNWYRQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDISTYFCQQGNALPRTFGGGTKLEIKR-----------------------------------------------------------------------------------------------------------   -
               SCOP domains d1jfql1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1jfql2 L:109-215 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1jfqL01 L:1-107 Immunoglobulins                                                                            1jfqL02 L:108-210 Immunoglobulins                                                                      ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfq L   1 DIQMTQIPSSLSASLGDRVSISCRASQDINNFLNWYQQKPDGTIKLLIYFTSRSQSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNALPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECA 215
                                    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)
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  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM03_MOUSE | P01747)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain L   (KV5AF_MOUSE | P01648)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

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  Cis Peptide Bonds
    Arg H:496 - Pro H:497   [ RasMol ]  
    Glu H:456 - Pro H:457   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Phe H:454 - Pro H:455   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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(-) Related Entries Specified in the PDB File

6fab ANTIGEN-BINDING FRAGMENT OF THE MURINE ANTI-PHENYLARSONATE ANTIBODY 36-71, "FAB 36-71"