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(-) Description

Title :  N1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITROPHENYL) ACETATE
 
Authors :  R. Mizutani, Y. Satow
Date :  23 Jun 95  (Deposition) - 11 Jul 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Mizutani, K. Miura, T. Nakayama, I. Shimada, Y. Arata, Y. Satow
Three-Dimensional Structures Of The Fab Fragment Of Murine N1G9 Antibody From The Primary Immune Response And Of Its Complex With (4-Hydroxy-3-Nitrophenyl)Acetate.
J. Mol. Biol. V. 254 208 1995
PubMed-ID: 7490744  |  Reference-DOI: 10.1006/JMBI.1995.0612
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N1G9 (IGG1-LAMBDA)
    ChainsL
    FragmentFAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainC57BL/6
 
Molecule 2 - N1G9 (IGG1-LAMBDA)
    ChainsH
    FragmentFAB FRAGMENT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainC57BL/6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NPA1Ligand/Ion2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS H:38 , ARG H:40 , ARG H:43 , LYS H:63 , HOH H:328 , PRO L:112 , LYS L:113BINDING SITE FOR RESIDUE SO4 H 301
2AC2SOFTWARETRP H:33 , HIS H:35 , ARG H:50 , LYS H:59 , TYR H:99 , TYR H:101 , SER H:105 , SER H:165 , HOH H:357 , HOH H:370 , TRP L:93 , TRP L:98BINDING SITE FOR RESIDUE NPA H 302

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:147 -H:202
3L:22 -L:90
4L:137 -L:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr L:143 -Pro L:144
2Phe H:153 -Pro H:154
3Glu H:155 -Pro H:156
4Trp H:195 -Pro H:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NGP)

(-) 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:215
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:215
                                                                                                                                                 139                                                                                               
                                    29        39        49        59        69        79        89        99       109       119       129       139         -         -         -         -         -         -         -         -         -     
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS-----------------------------------------------------------------------------------------------   -
               SCOP domains d1ngph1 H:1-120 Immunoglobulin heavy chain variable domain, VH                                                          d1ngph2 H:121-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1ngpH01 H:1-120 Immunoglobulins                                                                                         1ngpH02 H:121-219 Immunoglobulins                                                             - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee........eeeeeeee..............eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee........eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ngp H   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 145       155       165       175       185       195       205       215     
                                                                                                                                                                135|                                                                               
                                                                                                                                                                 141                                                                               

Chain L from PDB  Type:PROTEIN  Length:211
 aligned with G0YP42_MOUSE | G0YP42 from UniProtKB/TrEMBL  Length:234

    Alignment length:211
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
         G0YP42_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRVSGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSR 230
               SCOP domains d1ngpl1 L:1-109 Immunoglobulin light chain lambda variable domain, VL-lambda                                 d1ngpl2 L:110-211 Immunoglobulin light chain lambda constant domain, CL-lambda                         SCOP domains
               CATH domains 1ngpL01 L:1-110 Immunoglobulins                                                                               1ngpL02 L:111-210 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eee..eeeee...eeeeeeee...........eeeeee...eeeeee.............eeeeee..eeeeeee.......eeeeeeee....eee...eeeeee.......eeeee..........eeeeeeeee......eeeeeee........eee............-------hhhhhhh..eeeeeeee..eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeee--------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ngp L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSR 211
                                    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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM07_MOUSE | P01751)
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.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

Chain L   (G0YP42_MOUSE | G0YP42)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6v 1a6w 1ngq 1nqb 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 2bjm
UniProtKB/TrEMBL
        G0YP42_MOUSE | G0YP421etz 1ngq 1pg7

(-) Related Entries Specified in the PDB File

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