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(-) Description

Title :  ANTI HIV1 PROTEASE FAB
 
Authors :  J. Lescar, G. A. Bentley
Date :  06 May 99  (Deposition) - 12 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  H,I,L
Keywords :  Fab Fragment, Cross-Reactivity, Hiv1 Protease, Enzyme Inhibition, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lescar, J. Brynda, P. Rezacova, R. Stouracova, M. M. Riottot, V. Chitarra, M. Fabry, M. Horejsi, J. Sedlacek, G. A. Bentley
Inhibition Of The Hiv-1 And Hiv-2 Proteases By A Monoclonal Antibody.
Protein Sci. V. 8 2686 1999
PubMed-ID: 10631984
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (IGG1 ANTIBODY 1696 (LIGHT CHAIN))
    Cell LineHYBRIDOMA
    ChainsL
    FragmentFAB
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB/C
    SynonymIMMUNOGLOBULIN, IGG1
 
Molecule 2 - PROTEIN (IGG1 ANTIBODY 1696 (VARIABLE HEAVY CHAIN))
    Cell LineHYBRIDOMA
    ChainsH
    FragmentFAB
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB/C
    SynonymIMMUNOGLOBULIN, IGG1
 
Molecule 3 - PROTEIN (IGG1 ANTIBODY 1696 (CONSTANT HEAVY CHAIN))
    Cell LineHYBRIDOMA
    ChainsI
    FragmentFAB
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB/C
    SynonymIMMUNOGLOBULIN, IGG1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HIL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CL7)

(-) Sites  (0, 0)

(no "Site" information available for 1CL7)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2I:147 -I:202
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe I:153 -Pro I:154
5Glu I:155 -Pro I:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CL7)

(-) Exons   (0, 0)

(no "Exon" information available for 1CL7)

(-) 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:135
                                                                                                                                                                        
               SCOP domains d1cl7h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1cl7.1         SCOP domains
               CATH domains 1cl7H00 H:1-128 Immunoglobulins                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhh...eeeeee....eeeeee........eeeeee................eeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1cl7 H    1 QIQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSSAKTTPPSVYPLAPGS  128
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123     
                                                                              52A                            82A||               100A||                            
                                                                                                              82B|                100B|                            
                                                                                                               82C                 100C                            

Chain I from PDB  Type:PROTEIN  Length:82
 aligned with IGH1M_MOUSE | P01869 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:82
                                    30        40        50        60        70        80        90       100  
         IGH1M_MOUSE     21 SMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  102
               SCOP domains d1cl7.1 H:114-128,I: Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma SCOP domains
               CATH domains 1cl7I00 I:141-222 Immunoglobulins                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeehhh.....eee.........eeeeeeeeeehhhhhh...eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                1cl7 I  141 SMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  222
                                   150       160       170       180       190       200       210       220  

Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains d1cl7l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1cl7l2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1cl7L01 L:1-108 Immunoglobulins                                                                                  1cl7L02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...eeee..eeee.....eeeeeee............eeeeee......eeee......................eeeee........eeeeeee...........eeeee.........eee...hhhhhh.eeeeeee.........-----hhheee...eeeee...........eeeeeeeehhhhhh...eeeeee.............. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------eeeeee------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1cl7 L    1 DVLMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E                                                                                                                                                                                        

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CL7)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain I   (IGH1M_MOUSE | P01869)
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:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0001788    antibody-dependent cellular cytotoxicity    Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
    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:0002455    humoral immune response mediated by circulating immunoglobulin    An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.
    GO:0016064    immunoglobulin mediated immune response    An immune response mediated by immunoglobulins, whether cell-bound or in solution.
    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.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0001812    positive regulation of type I hypersensitivity    Any process that activates or increases the frequency, rate or extent of type I hypersensitivity, a type of inflammatory response.
    GO:0001798    positive regulation of type IIa hypersensitivity    Any process that activates or increases the frequency, rate or extent of type IIa hypersensitivity, a type of inflammatory response.
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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGH1M_MOUSE | P0186915c8 1a0q 1a3l 1acy 1ae6 1c12 1cic 1ck0 1f11 1f58 1igy 1jhk 1jrh 1kc5 1kcr 1kcu 1ken 1l7t 1ors 1qfu 1ruq 1rur 1s5i 25c8 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CL7)