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(-) Description

Title :  M4L/Y(27D)D/Q89D/T94H MUTANT OF LEN
 
Authors :  P. R. Pokkuluri, X. Cai, M. Gu, F. J. Stevens, M. Schiffer
Date :  03 Feb 00  (Deposition) - 03 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Kappa-4 Immunoglobulin Light Chain, Mutant, Aspartic Acid In Beta-Sheet, Protein Stability, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. R. Pokkuluri, M. Gu, X. Cai, R. Raffen, F. J. Stevens, M. Schiffer
Factors Contributing To Decreased Protein Stability When Aspartic Acid Residues Are In Beta-Sheet Regions.
Protein Sci. V. 11 1687 2002
PubMed-ID: 12070321  |  Reference-DOI: 10.1110/PS.4920102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KAPPA-4 IMMUNOGLOBULIN (LIGHT CHAIN)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPASK40
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , ASP A:89 , HOH A:967 , IPA B:500 , HOH B:903BINDING SITE FOR RESIDUE IPA A 499
2AC2SOFTWAREIPA A:499 , HOH A:908 , TYR B:336 , ASP B:389BINDING SITE FOR RESIDUE IPA B 500

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2B:323 -B:388

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2His A:94 -Pro A:95
3Ser B:307 -Pro B:308
4His B:394 -Pro B:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EEU)

(-) 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 A from PDB  Type:PROTEIN  Length:112
 aligned with KV401_HUMAN | P06312 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:112
                                                                                                                              121           
                                    30        40        50        60        70        80        90       100       110       120|        -  
         KV401_HUMAN     21 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP-----------    -
               SCOP domains d1eeua_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                            SCOP domains
               CATH domains 1eeuA00 A:1-106 Immunoglobulins                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                1eeu A    1 DIVLTQSPDSLAVSLGERATINCKSSQSVLDSSNSKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCDQYYSHPYSFGQGTKLEI  106
                                    10        20       27C|||     34        44        54        64        74        84        94       104  
                                                     27A|||||                                                                               
                                                      27B||||                                                                               
                                                       27C|||                                                                               
                                                        27D||                                                                               
                                                         27E|                                                                               
                                                          27F                                                                               

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with KV401_HUMAN | P06312 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:113
                                                                                                                              121            
                                    30        40        50        60        70        80        90       100       110       120|        -   
         KV401_HUMAN     21 DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP------------    -
               SCOP domains d1eeub_ B: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 1eeuB00 B:301-407 Immunoglobulins                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                1eeu B  301 DIVLTQSPDSLAVSLGERATINCKSSQSVLDSSNSKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCDQYYSHPYSFGQGTKLEIK  407
                                   310       320      327C|||    334       344       354       364       374       384       394       404   
                                                    327A|||||                                                                                
                                                     327B||||                                                                                
                                                      327C|||                                                                                
                                                       327D||                                                                                
                                                        327E|                                                                                
                                                         327F                                                                                

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KV401_HUMAN | P06312)
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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002377    immunoglobulin production    The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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
        KV401_HUMAN | P063121dh6 1eeq 1efq 1ek3 1lve 1qac 2lve 3lve 4lve 5lve

(-) Related Entries Specified in the PDB File

1eeq M4L/Y27DD/T94H MUTANT OF LEN IS ISOMORPHOUS TO THE PRESENT ENTRY. THE WATER MOLECULES 501-861 CORRESPOND TO THE SAME WATER IN THE ENTRY 1EEQ AND WATERS 901-968 ARE WATER MOLECULES THAT ARE NEW IN THIS ENTRY.