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(-) Description

Title :  SPE7:ANTHRONE COMPLEX
 
Authors :  L. C. James, D. S. Tawfik
Date :  04 Feb 05  (Deposition) - 18 Aug 05  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  H,L
Biol. Unit 1:  H,L  (4x)
Keywords :  Immune System, Encounter Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. C. James, D. S. Tawfik
Structure And Kinetics Of A Transient Antibody Binding Intermediate Reveal A Kinetic Discrimination Mechanism In Antigen Recognition
Proc. Natl. Acad. Sci. Usa V. 102 12730 2005
PubMed-ID: 16129832  |  Reference-DOI: 10.1073/PNAS.0500909102

(-) Compounds

Molecule 1 - IGE SPE7 LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentLIGHT CHAIN, RESIDUES 1-110
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - IGE SPE7 HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentHEAVY CHAIN, RESIDUES 1-120
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsANTHRONE ATTACHED

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit HL
Biological Unit 1 (4x)HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ANF1Ligand/IonANTHRONE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ANF4Ligand/IonANTHRONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , TYR H:101 , TYR L:34 , ASN L:36 , TRP L:93BINDING SITE FOR RESIDUE ANF H 500

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1H:22 -H:96
2L:22 -L:90

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu H:1 -Val H:2
2Val H:118 -Ser H:119
3Leu L:109 -Glu L:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BJM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BJM)

(-) Exons   (0, 0)

(no "Exon" information available for 2BJM)

(-) 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 H from PDB  Type:PROTEIN  Length:120
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:120
                                    29        39        49        59        69        79        89        99       109       119       129       139
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS 139
               SCOP domains d2bjmh_ H: Immunoglobulin heavy chain variable domain, VH                                                                SCOP domains
               CATH domains 2bjmH00 H:1-120 Immunoglobulins                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee.........eeeeee...eeee....................eeeeee....eeeeee...hhhhheeeeee................eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bjm H   1 EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSS 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain L from PDB  Type:PROTEIN  Length:110
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:110
                                    29        39        49        59        69        79        89        99       109       119       129
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG 129
               SCOP domains d2bjml_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                        SCOP domains
               CATH domains 2bjmL00 L:1-110 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeeeeee...........eeeeee...eeeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeee....eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2bjm L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVLE 110
                                    10        20        30        40        50        60        70        80        90       100       110

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BJM)

(-) Gene Ontology  (12, 13)

Asymmetric 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   (LV1B_MOUSE | P01724)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6v 1a6w 1ngp 1ngq 1nqb 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw
        LV1B_MOUSE | P017241a6u 1a6v 1a6w 1dl7 1oaq 1oar 1oau 1oax 1oay 1oaz 1ocw 1q0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BJM)