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(-) Description

Title :  IDIOTOPIC ANTIBODY D1.3 FV FRAGMENT-ANTIIDIOTOPIC ANTIBODY E5.2 FV FRAGMENT COMPLEX
 
Authors :  B. C. Braden, B. A. Fields, X. Ysern, W. Dall'Acqua, F. A. Goldbaum, R. J. R. A. Mariuzza
Date :  13 Apr 96  (Deposition) - 17 Aug 96  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Complex (Idiotope-Antiidiotope), Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. C. Braden, B. A. Fields, X. Ysern, W. Dall'Acqua, F. A. Goldbaum, R. J. Poljak, R. A. Mariuzza
Crystal Structure Of An Fv-Fv Idiotope-Anti-Idiotope Comple At 1. 9 A Resolution.
J. Mol. Biol. V. 264 137 1996
PubMed-ID: 8950273  |  Reference-DOI: 10.1006/JMBI.1996.0629
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FV D1.3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: IGG1, KAPPA
    Strain: BALB-C
 
Molecule 2 - FV D1.3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: IGG1, KAPPA
    Strain: BALB/C
 
Molecule 3 - FV E5.2
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: IGG1, KAPPA
    Strain: BALB-C
 
Molecule 4 - FV E5.2
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: IGG1, KAPPA
    Strain: BALB/C

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:100 , HOH B:1011 , HIS D:33 , ASP D:52BINDING SITE FOR RESIDUE ZN D 1158
2AC2SOFTWAREASP C:1 , GLN C:3BINDING SITE FOR RESIDUE ZN C 1159
3AC3SOFTWAREHIS B:86 , ASP B:88BINDING SITE FOR RESIDUE ZN B 1160

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:22 -B:95
3C:23 -C:88
4D:22 -D:92

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Ser C:7 -Pro C:8
4Leu C:94 -Pro C:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DVF)

(-) 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:107
 aligned with KV5A3_MOUSE | P01635 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:107
                                                                                                                        115            
                                    30        40        50        60        70        80        90       100       110    |    -       
         KV5A3_MOUSE     21 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTP------------    -
               SCOP domains d1dvfa_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1dvfA00 A:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                1dvf A    1 DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK  107
                                    10        20        30        40        50        60        70        80        90       100       


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:116
                                                                                                                         115                    
                                    29        39        49        59        69        79        89        99       109     |   -         -      
         HVM44_MOUSE     20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA--------------------    -
               SCOP domains d1dvfb_ B: Immunoglobulin heavy chain variable domain, VH                                                            SCOP domains
               CATH domains 1dvfB00 B:1-116 Immunoglobulins                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.......eeeeeee.....eeeeeee.....eee.......eeeeee....eeeeee....hhh.eeeeeeeee..eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                1dvf B    1 QVQLQESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGNTDYNSALKSRLSISKDNSKSQVFLKMNSLHTDDTARYYCARERDYRLDYWGQGTTLTVSS  116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C from PDB  Type:PROTEIN  Length:107
 aligned with KV5AD_MOUSE | P01646 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:107
                                    10        20        30        40        50        60        70        80        90       100       
         KV5AD_MOUSE      1 DIQMTQSTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGYMLPRTFGGGTKLEIK  107
               SCOP domains d1dvfc_ C: Immunoglobulin light chain kappa variable domain, VL-kappa                                       SCOP domains
               CATH domains 1dvfC00 C:1-107 Immunoglobulins                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee....hhh..eeeeee............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                1dvf C    1 DIQLTQSPSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIK  107
                                    10        20        30        40        50        60        70        80        90       100       


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with A0NA69_MOUSE | A0NA69 from UniProtKB/TrEMBL  Length:122

    Alignment length:121
                                                                                                                           117               118 122 
                                    29        39        49        59        69        79        89        99       109       | -         -     | 122 
        A0NA69_MOUSE     20 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAT-----------------VPLVL-    -
               SCOP domains d1dvfd_ D: Immunoglobulin heavy chain variable domain, VH                                                                 SCOP domains
               CATH domains 1dvfD00 D:1-112 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eee...eeeeeeeee...hhh.eeeeeee.....eeeeeeee.....eee.hhh...eeeeeehhh.eeeeeee...hhh.eeeeee..................eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                1dvf D    1 QVQLQQSGTELVKSGASVKLSCTASGFNIKDTHMNWVKQRPEQGLEWIGRIDPANGNIQYDPKFRGKATITADTSSNTAYLQLSSLTSEDTAVYYCATKVIYYQGRGAMDYWGQGTTLTVS  112
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111 
                                                                              52A                            82A||               100A||||            
                                                                                                              82B|                100B|||            
                                                                                                               82C                 100C||            
                                                                                                                                    100D|            
                                                                                                                                     100E
   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  (3, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (KV5A3_MOUSE | P01635)
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 B   (HVM44_MOUSE | P01820)
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 C   (KV5AD_MOUSE | P01646)
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 D   (A0NA69_MOUSE | A0NA69)

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  1dvf
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  KV5AD_MOUSE | P01646
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM44_MOUSE | P01820: 1a2y 1a7n 1a7o 1a7p 1a7q 1a7r 1dl7 1g7h 1g7i 1g7j 1g7l 1g7m 1kir 1p4b 1p4i 1vfa 1vfb 43c9 43ca
        KV5A3_MOUSE | P01635: 1a2y 1a7n 1a7o 1a7p 1a7q 1a7r 1kip 1kiq 1qbl 1qbm 1vfa 1vfb 1wej

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DVF)