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(-) Description

Title :  AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX
 
Authors :  J. N. Herron, X. M. He, D. W. Ballard, P. R. Blier, P. E. Pace, A. L. M. Bothw E. W. Voss Junior, A. B. Edmundson
Date :  16 Mar 93  (Deposition) - 31 Jan 94  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym./Biol. Unit :  D,H,L
Keywords :  Protein-Dna Complex, Single Strand, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Herron, X. M. He, D. W. Ballard, P. R. Blier, P. E. Pace, A. L. Bothwell, E. W. Voss Jr. , A. B. Edmundson
An Autoantibody To Single-Stranded Dna: Comparison Of The Three-Dimensional Structures Of The Unliganded Fab And A Deoxynucleotide-Fab Complex.
Proteins V. 11 159 1991
PubMed-ID: 1749770  |  Reference-DOI: 10.1002/PROT.340110302
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*TP*T)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTEIN (FAB (BV04-01) AUTOANTIBODY-LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PROTEIN (FAB (BV04-01) AUTOANTIBODY-HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : DHL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1HD1UNKNOWNTHR H:31 , ASN H:32 , ALA H:33NULL
2HD2UNKNOWNARG H:52 , SER H:53 , ASN H:56NULL
3HD3UNKNOWNASP H:101 , GLN H:102 , THR H:103 , GLY H:104 , THR H:105 , ALA H:106 , TRP H:107NULL
4LD1UNKNOWNHIS L:31 , SER L:32 , TYR L:37 , HIS L:39NULL
5LD3UNKNOWNSER L:96 , THR L:97 , HIS L:98 , VAL L:99NULL

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:98
2H:148 -H:203
3L:23 -L:93
4L:139 -L:199
5L:219 -H:136

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:154 -Pro H:155
5Trp H:196 -Pro H:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CBV)

(-) 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 D from PDB  Type:DNA  Length:3
                                   
                 1cbv D   1 TTT   3


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1cbvh1 H:1-122 Immunoglobulin heavy chain variable domain, VH                                                            d1cbvh2 H:123-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1cbvH01 H:1-121 Immunoglobulins                                                                                          1cbvH02 H:122-219 Immunoglobulins                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeee..eee.....eeeeeeee.......eeeeeeee..eeeeeeeeee......eeeee.....------hhhhheeeeeee.......eeeeee..........eeeeeeeeeee.......eeeee...........eeeeeeeeeeeeeeeeeeee......eeeeeeeeee..eeeeeeeeeehhhhhhhh--------....eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------eeeeeee-----------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeee------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cbv H   1 EVQPVETGGGLVQPKGSLKLSCAASGFSFNTNAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQNMLYLQMNNLKTEDTAMYYCVRDQTGTAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLE 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
               SCOP domains d1cbvl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1cbvl2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1cbvL01 L:1-113 Immunoglobulins                                                                                  1cbvL02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.eeeee.....eeeeeeee..........eeeeeeee..eeeeeeeee..eee.......eeeee..eeeeee........eeeeeeee....eeeeeeeeeeee......eeeee..hhhhhhh..eeeeeeeeee.....eeeeeee......eeeeeeeeee....eeeeeeeeeehhhhhhh..eeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cbv L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 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  (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 1CBV)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (A2NHM3_MOUSE | A2NHM3)

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    Phe H:154 - Pro H:155   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:196 - Pro H:197   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
    Val L:99 - Pro L:100   [ RasMol ]  
 

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  1cbv
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  A2NHM3_MOUSE | A2NHM3
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  IGG2B_MOUSE | P01867
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        IGG2B_MOUSE | P01867: 1cf8 1cic 1etz 1fj1 1fl3 1hq4 1mam 1nbv 1osp 1ub5 1ub6 1ynk 1ynl 1ztx 2gjz 2gk0 2q8a 2q8b 2rgs 3cfd 3cfe
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

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