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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-TESTOSTERONE FAB FRAGMENT
 
Authors :  J. Valjakka, A. Hemminki, S. Niemi, H. Soderlund, K. Takkinen, J. Rouvinen
Date :  17 Mar 02  (Deposition) - 02 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Anti-Testosterone, Fab Fragment, Affinity And Specificity Matured, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Valjakka, A. Hemminki, S. Niemi, H. Soderlund, K. Takkinen, J. Rouvinen
Crystal Structure Of An In Vitro Affinity- And Specificity-Matured Anti-Testosterone Fab In Complex With Testosterone. Improved Affinity Results From Small Structural Changes Within The Variable Domains
J. Biol. Chem. V. 277 44021 2002
PubMed-ID: 12196551  |  Reference-DOI: 10.1074/JBC.M208392200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-TESTOSTERONE (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
    Fragment: FAB77 FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTI-TESTOSTERONE (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
    Fragment: FAB77 FRAGMENT
    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 1L7T)

(-) Sites  (0, 0)

(no "Site" information available for 1L7T)

(-) 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 1L7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L7T)

(-) Exons   (0, 0)

(no "Exon" information available for 1L7T)

(-) 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 d1l7th1 H:1-118 Immunoglobulin heavy chain variable domai n, VH                                                        d1l7th2 H:119-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                                     SCOP domains
               CATH domains 1l7tH01 H:1-118 Immunoglobulins                                                                                        1l7tH02 H:119-217 Immunoglobulins                                                                  ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.....e-ee........eeeee....eeeeee...hhhhheeeeeee..............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...-------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l7t H   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSRYALSWVRQTADKRLEWVASIVSGGNT-YYSGSVKGRFTISRDIARNILYLQMSSLRSEDTAMYYCARAYYGYVGLVHWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP-------------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 d1l7tl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1l7tl2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1l7tL01 L:1-113 Immunoglobulins                                                                                  1l7tL02 L:114-215 Immunoglobulins                                                                     ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l7t L   1 DVVVTQTPLSLPVSLGDQASISCRSSEVIVTRNGYTPIEWYLQKPGQSPKLLIYKAYKRFPGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFDGSTVPPKFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRDEC 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 1L7T)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q91Z05_MOUSE | Q91Z05)

Chain L   (Q65ZC0_MOUSE | Q65ZC0)

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(no "Sites" information available for 1l7t)
 
  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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  1l7t
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  Q65ZC0_MOUSE | Q65ZC0
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  Q91Z05_MOUSE | Q91Z05
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGH1M_MOUSE | P01869: 15c8 1a0q 1a3l 1acy 1ae6 1c12 1cic 1ck0 1cl7 1f11 1f58 1igy 1jhk 1jrh 1kc5 1kcr 1kcu 1ken 1ors 1qfu 1ruq 1rur 1s5i 25c8 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1
        Q65ZC0_MOUSE | Q65ZC0: 2g60
UniProtKB/TrEMBL
        Q65ZC0_MOUSE | Q65ZC0: 1i9i 1i9j 1lo2 1lo3 1lo4 1t66 2gjz 2gk0
        Q91Z05_MOUSE | Q91Z05: 1i9i 1i9j 1jgu 1jgv 1lo2 1lo3 1lo4 1t66 2gk0

(-) Related Entries Specified in the PDB File

1l7s CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-TESTOSTERONE FAB IN COMPLEX WITH TESTOSTERONE