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(-) Description

Title :  NATIVE CRYSTAL STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT
 
Authors :  J. Valjakka, K. Takkinenz, T. Teerinen, H. Soderlund, J. Rouvinen
Date :  20 Mar 01  (Deposition) - 20 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab Fragment, Anti-Testosterone, Recombinant, Monoclonal, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Valjakka, K. Takkinenz, T. Teerinen, H. Soderlund, J. Rouvinen
Structural Insights Into Steroid Hormone Binding: The Crystal Structure Of A Recombinant Anti-Testosterone Fab Fragment In Free And Testosterone-Bound Forms.
J. Biol. Chem. V. 277 4183 2002
PubMed-ID: 11707437  |  Reference-DOI: 10.1074/JBC.M105579200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKTAC
    Expression System Strain: RV308
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKTAC
    Expression System Strain: RV308
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1I9I)

(-) Sites  (0, 0)

(no "Site" information available for 1I9I)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2H:145 -H:200
3L:23 -L:93
4L:139 -L:199
5L:219 -H:220

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:151 -Pro H:152
5Glu H:153 -Pro H:154
6Trp H:193 -Pro H:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I9I)

(-) Exons   (0, 0)

(no "Exon" information available for 1I9I)

(-) 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:220
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:234
                                                                                                                                121                                                                                                                                   
                                                                                                                              120 |                                                                                                                                   
                                    29        39        49        59        69        79        89        99       109       119| |    128       138       148       158       168       178       188       198       208       218       228       238       248    
         Q91Z05_MOUSE    20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCARELW-LRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKEC 252
               SCOP domains d1i9ih1 H:1-118 Immunoglobulin heavy chain variable domai n, VH                                                        d1i9ih2 H:119-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                                     SCOP domains
               CATH domains 1i9iH01 H:1-118 Immunoglobulins                                                                                        1i9iH02 H:119-217 Immunoglobulins                                                                  ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeee.....e-ee.......eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.........hhhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...-------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i9i H   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSTYALSWVRQTADKRLEWVASIVSGGNT-YYSGSVKGRFTISRDIARNILYLQMSSLRSEDTAMYYCAREYYGYVGLAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP-------------RDC 220
                                    10        20        30        40        50      | 59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       | -         - |  
                                                                                   57 |                                                                                                                                                            217           218  
                                                                                     58                                                                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
         Q65ZC0_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC 219
               SCOP domains d1i9il1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1i9il2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1i9iL01 L:1-113 Immunoglobulins                                                                                  -1i9iL02 L:115-214 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9i L   1 DVVVTQTPLSLPVSLGDQASISCRSSQSIVHSNGNSYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I9I)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1I9I)

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Asymmetric/Biological Unit
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  Sites
(no "Sites" information available for 1i9i)
 
  Cis Peptide Bonds
    Glu H:153 - Pro H:154   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:193 - Pro H:194   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
    Val L:99 - Pro L:100   [ RasMol ]  
 

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  1i9i
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  Q65ZC0_MOUSE | Q65ZC0
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    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q91Z05_MOUSE | Q91Z05
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q65ZC0_MOUSE | Q65ZC0: 2g60
UniProtKB/TrEMBL
        Q65ZC0_MOUSE | Q65ZC0: 1i9j 1l7t 1lo2 1lo3 1lo4 1t66 2gjz 2gk0
        Q91Z05_MOUSE | Q91Z05: 1i9j 1jgu 1jgv 1l7t 1lo2 1lo3 1lo4 1t66 2gk0

(-) Related Entries Specified in the PDB File

1i9j 1I9J CONTAINS TESTOSTERONE COMPLEX STRUCTURE OF THE SAME PROTEIN