Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FAB-ESTRADIOL COMPLEXES
 
Authors :  C. Monnet, F. Bettsworth, E. A. Stura, M. -H. Le Du, R. Menez, L. Derrien, S. Zinn-Justin, B. Gilquin, G. Sibai, N. Battail-Poirot, M. Jolivet, A. Menez, M. Arnaud, F. Ducancel, J. B. Charbonnier
Date :  24 Jul 01  (Deposition) - 06 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Igg Fold, Antibody-Hapten Complex, Estradiol, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Monnet, F. Bettsworth, E. A. Stura, M. H. Du, R. Menez, L. Derrien, S. Zinn-Justin, B. Gilquin, G. Sibai, N. Battail-Poirot, M. Jolivet, A. Menez, M. Arnaud, F. Ducancel, J. B. Charbonnier
Highly Specific Anti-Estradiol Antibodies: Structural Characterisation And Binding Diversity.
J. Mol. Biol. V. 315 699 2002
PubMed-ID: 11812141  |  Reference-DOI: 10.1006/JMBI.2001.5284
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL ANTI-ESTRADIOL 17E12E5 IMMUNOGLOBULIN KAPPA CHAIN
    ChainsL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymFAB' 17E12, LIGHT CHAIN
 
Molecule 2 - MONOCLONAL ANTI-ESTRADIOL 17E12E5 IMMUNOGLOBULIN GAMMA-1 CHAIN
    ChainsH
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymFAB' 17E12, HEAVY CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EST1Ligand/IonESTRADIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:35 , GLU H:99 , LYS H:100 , ASP H:101 , TYR L:36 , LEU L:46 , HIS L:89 , PHE L:91BINDING SITE FOR RESIDUE EST H 350

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:143 -H:209
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Thr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:149 -Pro H:150
5Glu H:151 -Pro H:152
6Trp H:201 -Pro H:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90  1L:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 1JNN)

(-) 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:214
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:220
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
         Q99LC4_MOUSE    20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCARSSYYSYDLFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 239
               SCOP domains d1jnnh1 H:1-114 Immunoglobulin heavy chain variable domain, VH                                                          d1jnnh2 H:115-229 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1jnnH01 H:1-114 Immunoglobulins                                                                                         1jnnH02 H:115-228 Immunoglobulins                                                                  - CATH domains
               Pfam domains -V-set-1jnnH02 H:2-112                                                                                                --------------C1-set-1jnnH01 H:127-221                                                          ------ Pfam domains
         Sec.struct. author ..eee....eee.....eeeeeeee..hhhhh.eeeeee.....eee.ee........eehhhhhh.eeeee.hhh.eeeeee...hhhhheeeeeee.....------....eeeee........eeeee..........eeeeeeeeeee.....eeee........eeee........eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnn H   1 EVQLQQSGAELVKPGASVRLSCSASGFNIKDTYMFWVKQRPEQGLDWIGRINPANGISKYDPRFQGKATLTADTSSNTAYLQLDNLTSEDTAVYYCAIEKDLP------WGQGTLVTVSVAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 229
                                    10        20        30        40        50        60        70        80        90       100  |    104       114       124       134  ||   146       157||     172       184       194  |||| 207       217      |229
                                                                                                                                103    104                              137|            155|||    170|      181|          197|||                  224|  
                                                                                                                                                                         140             157||     172       184           200||                   227  
                                                                                                                                                                                          158|                              201|                        
                                                                                                                                                                                           163                               203                        

Chain L from PDB  Type:PROTEIN  Length:211
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:211
                                                                                                                                        1                                                                                                      
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102 
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 103
               SCOP domains d1jnnl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1jnnl2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1jnnL01 L:1-108 Immunoglobulins                                                                             1jnnL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ---V-set-1jnnL02 L:4-106                                                                                  ------------C1-set-1jnnL01 L:119-206                                                                ----- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee....hhhhh.eeeeeeeee......eeeeee....ee...eeeee..........eeeeeeeeehhhhhh...eeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnn L   1 QIVMTQTPASLSASVGETVTITCRASGNIYNYLAWYQQKQGKSPQLLVYNAKTLVDGVPLRFSGSGSGTQYSLKINSLQPEDFGNYYCHHFWNTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    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:211
 aligned with Q7TS98_MOUSE | Q7TS98 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
         Q7TS98_MOUSE    23 DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 233
               SCOP domains d1jnnl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1jnnl2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1jnnL01 L:1-108 Immunoglobulins                                                                             1jnnL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ---V-set-1jnnL02 L:4-106                                                                                  ------------C1-set-1jnnL01 L:119-206                                                                ----- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee....hhhhh.eeeeeeeee......eeeeee....ee...eeeee..........eeeeeeeeehhhhhh...eeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jnn L   1 QIVMTQTPASLSASVGETVTITCRASGNIYNYLAWYQQKQGKSPQLLVYNAKTLVDGVPLRFSGSGSGTQYSLKINSLQPEDFGNYYCHHFWNTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 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)
  - → 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  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q99LC4_MOUSE | Q99LC4)

Chain L   (Q7TS98_MOUSE | Q7TS98)

Chain L   (IGKC_MOUSE | P01837)
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:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    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.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EST  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:151 - Pro H:152   [ RasMol ]  
    Phe H:149 - Pro H:150   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Thr L:94 - Pro L:95   [ RasMol ]  
    Trp H:201 - Pro H:203   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1jnn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IGKC_MOUSE | P01837
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  Q7TS98_MOUSE | Q7TS98
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q99LC4_MOUSE | Q99LC4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IGKC_MOUSE | P01837
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q7TS98_MOUSE | Q7TS98
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q99LC4_MOUSE | Q99LC4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IGKC_MOUSE | P0183715c8 1a0q 1a3l 1ahw 1ai1 1aif 1c12 1cf8 1cfn 1cfq 1cfs 1cft 1cic 1ck0 1ct8 1dqj 1dqm 1dqq 1e4w 1e4x 1ehl 1emt 1f11 1fai 1fbi 1fdl 1fe8 1fgn 1fj1 1fl3 1fns 1frg 1fsk 1gpo 1hh6 1hh9 1hi6 1i8m 1iai 1igy 1jnl 1jrh 1k4c 1k4d 1kb5 1kc5 1kcr 1kcs 1kcu 1kcv 1ken 1kno 1lo0 1mf2 1mh5 1mlb 1mlc 1n5y 1n6q 1nby 1nbz 1ndg 1ndm 1oak 1ob1 1orq 1ors 1osp 1ots 1ott 1otu 1p2c 1p7k 1psk 1q9o 1q9w 1qgc 1r0a 1r24 1r3i 1r3j 1r3k 1r3l 1rih 1ruq 1rur 1s5h 1seq 1t03 1t4k 1ub5 1ub6 1uwx 1xf2 1xf3 1xf4 1xgp 1xgq 1xgu 25c8 2a6d 2a6k 2adf 2adj 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1 2bob 2boc 2ck0 2f19 2fr4 2g5b 2h8p 2hg5 2hrp 2mpa 2nr6 2q76 2r1w 2r1y 2r23 2r2b 2uyl 2v17 2v7h 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 2vl5 2vq1 2vwe 2w60 2w65 2w9d 2w9e 2z91 2z92 2z93 2zjs 35c8 3bae 3bgf 3bkc 3bkj 3bkm 3bpc 3bqu 3bsz 3bt2 3bz4 3c5s 3c6s 3cfb 3cfc 3cfd 3cfe 3ck0 3cle 3clf 3cmo 3cvh 3cvi 3d9a 3ejz 3eot 3f7v 3f7y 3fb6 3hfm 4kk5 4kk8 4qnp 4zxb 6fab
        Q7TS98_MOUSE | Q7TS981d5b 1d5i 1d6v 2exp 2exq 5vpl
        Q99LC4_MOUSE | Q99LC41afv 3hkf
UniProtKB/TrEMBL
        Q7TS98_MOUSE | Q7TS981i8m 1jgl 1jhk 1jnl 3bgf 3j42 4kvc
        Q99LC4_MOUSE | Q99LC41ae6 1e6j 1f58 1gig 1jhk 1jnl 2a1w 2ntf 2vir 2vis 2vit 4q0x

(-) Related Entries Specified in the PDB File

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