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(-) Description

Title :  FV STRUCTURE OF THE IGE SPE-7 IN COMPLEX WITH DNP-SER (IMMUNISING HAPTEN)
 
Authors :  L. C. James, P. Roversi, D. Tawfik
Date :  21 Jan 03  (Deposition) - 15 Jan 04  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  H,I,J,K,L,M,N,O
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Biol. Unit 3:  J,N  (1x)
Biol. Unit 4:  K,O  (1x)
Keywords :  Immune System, Antibody/Complex, Antibody, Allergy, Ige, Conformational Diversity, Multispecificity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. C. James, P. Roversi, D. Tawfik
Antibody Multispecificity Mediated By Conformational Diversity
Science V. 299 1362 2003
PubMed-ID: 12610298  |  Reference-DOI: 10.1126/SCIENCE.1079731

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN E
    ChainsH, I, J, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFV REGION, RESIDUES 1-122
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsEXPRESSED AS RECOMBINANT FV IN E.COLI
 
Molecule 2 - IMMUNOGLOBULIN E
    ChainsL, M, N, O
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFV REGION, RESIDUES 1-110
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsEXPRESSED AS RECOMBINANT FV IN E.COLI

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit HIJKLMNO
Biological Unit 1 (1x)H   L   
Biological Unit 2 (1x) I   M  
Biological Unit 3 (1x)  J   N 
Biological Unit 4 (1x)   K   O

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1DNF2Ligand/Ion2,4-DINITROPHENOL
2IMD2Ligand/IonIMIDAZOLE
3SER2Mod. Amino AcidSERINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1DNF1Ligand/Ion2,4-DINITROPHENOL
2IMD1Ligand/IonIMIDAZOLE
3SER1Mod. Amino AcidSERINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1DNF-1Ligand/Ion2,4-DINITROPHENOL
2IMD-1Ligand/IonIMIDAZOLE
3SER-1Mod. Amino AcidSERINE
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1DNF1Ligand/Ion2,4-DINITROPHENOL
2IMD1Ligand/IonIMIDAZOLE
3SER1Mod. Amino AcidSERINE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1DNF-1Ligand/Ion2,4-DINITROPHENOL
2IMD-1Ligand/IonIMIDAZOLE
3SER-1Mod. Amino AcidSERINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , LYS H:59 , TYR H:105 , DNF H:501 , TRP L:93 , LEU O:68BINDING SITE FOR RESIDUE SER H 500
2AC2SOFTWARETRP H:33 , HIS H:35 , ARG H:50 , LYS H:59 , MET H:99 , TYR H:105 , SER H:500 , TYR L:34 , TRP L:93 , LEU L:98 , HOH L:2050BINDING SITE FOR RESIDUE DNF H 501
3AC3SOFTWARETRP J:33 , LYS J:59 , TYR J:105 , DNF J:501 , HOH J:2070 , LEU M:68 , TRP N:93BINDING SITE FOR RESIDUE SER J 500
4AC4SOFTWARETRP J:33 , HIS J:35 , ARG J:50 , LYS J:59 , MET J:99 , TYR J:105 , SER J:500 , TYR N:34 , TRP N:93 , LEU N:98 , HOH N:2025 , HOH N:2027BINDING SITE FOR RESIDUE DNF J 501
5AC5SOFTWAREGLU H:62 , ASN L:96 , HIS L:97BINDING SITE FOR RESIDUE IMD L 200
6AC6SOFTWAREGLU J:62 , ASN N:96 , HIS N:97BINDING SITE FOR RESIDUE IMD N 200

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1H:22 -H:96
2J:22 -J:96
3L:22 -L:90
4M:22 -M:90
5N:22 -N:90
6O:22 -O:90

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OAU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OAU)

(-) Sequences/Alignments

Asymmetric 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:123
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:123
                                                                                                                                                 139   
                                    29        39        49        59        69        79        89        99       109       119       129       139   
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS---   -
               SCOP domains d1oauh_ H: Immunoglobulin heavy chain variable domain, VH                                                                   SCOP domains
               CATH domains 1oauH00 H:1-122 Immunoglobulins                                                                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oau H   1 EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAAS 500
                                    10        20        30        40        50        60        70        80        90       100       110       120 ||
                                                                                                                                                   122|
                                                                                                                                                    500

Chain I from PDB  Type:PROTEIN  Length:22
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:112
                                    36        46        56        66        76        86        96       106       116       126       136  
          HVM07_MOUSE    27 GAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVS 138
               SCOP domains d1        oa               u    i_                                       I           : Immun       o   g  lo  bu SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------..---------------.----..-------------------------------------.-.-----------.......-------.---.--..--.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1oau I   8 GA--------VK---------------H----RP-------------------------------------A-M-----------VYYCARM-------F---G--TT--VS 119
                             |       -||       -       | -  ||     -         -         -         - | |     -     |  97 |     107   |  || -| 
                             9       18|              35   40|                                    79 |          93    99     107 111  ||  | 
                                      19                    41                                      81                              114|  | 
                                                                                                                                     115  | 
                                                                                                                                        118 

Chain J from PDB  Type:PROTEIN  Length:123
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:123
                                                                                                                                                 139   
                                    29        39        49        59        69        79        89        99       109       119       129       139   
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS---   -
               SCOP domains d1oauj_ J: Immunoglobulin heavy chain variable domain, VH                                                                   SCOP domains
               CATH domains 1oauJ00 J:1-122 Immunoglobulins                                                                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oau J   1 EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAAS 500
                                    10        20        30        40        50        60        70        80        90       100       110       120 ||
                                                                                                                                                   122|
                                                                                                                                                    500

Chain K from PDB  Type:PROTEIN  Length:22
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:113
                                    36        46        56        66        76        86        96       106       116       126       136   
          HVM07_MOUSE    27 GAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS 139
               SCOP domains d1        oa                    uk                                     _             K: Immu        n og  lo  b u SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------..--------------------..-------------------------------------.-.-----------.......--------.-..--..--.-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1oau K   8 GA--------VK--------------------RP-------------------------------------A-M-----------VYYCARM--------D-WG--TT--V-S 120
                             |       -||       -         -  ||     -         -         -         - | |     -     |  97 |       -| ||  || -| |
                             9       18|                   40|                                    79 |          93    99      108 ||  ||  | |
                                      19                    41                                      81                          110|  ||  | |
                                                                                                                                 111  ||  | |
                                                                                                                                    114|  | |
                                                                                                                                     115  | |
                                                                                                                                        118 |
                                                                                                                                          120

Chain L from PDB  Type:PROTEIN  Length:108
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oaul_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                      SCOP domains
               CATH domains 1oauL00 L:2-109 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oau L   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    11        21        31        41        51        61        71        81        91       101        

Chain M from PDB  Type:PROTEIN  Length:90
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:104
                                    34        44        54        64        74        84        94       104       114       124    
           LV1B_MOUSE    25 QESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oaum_ M: Immunoglobulin light chain lambda  v ariable domain, VL-lambda                                SCOP domains
               CATH domains 1oauM00 M:6-109 Immunoglobulins                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeee.......hhhhh..eeeee...eeeeee-.-..........eeeeee..eeeeeee..hhhhheeee.------------.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1oau M   6 QESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLI-G-NNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFC------------GTKLTVL 109
                                    15        25        35        45    | | 55        65        75        85    |    -       105    
                                                                       50 | |                                  90          103      
                                                                         52 |                                                       
                                                                           54                                                       

Chain N from PDB  Type:PROTEIN  Length:108
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oaun_ N: Immunoglobulin light chain lambda variable domain, VL-lambda                                      SCOP domains
               CATH domains 1oauN00 N:2-109 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oau N   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    11        21        31        41        51        61        71        81        91       101        

Chain O from PDB  Type:PROTEIN  Length:92
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:104
                                    34        44        54        64        74        84        94       104       114       124    
           LV1B_MOUSE    25 QESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oauo_ O: Immunoglobulin light chain lambda variable domain, VL-lambda                                  SCOP domains
               CATH domains 1oauO00 O:6-109 Immunoglobulins                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeee......hhhhh..eeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeee.------------.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1oau O   6 QESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFC------------GTKLTVL 109
                                    15        25        35        45        55        65        75        85    |    -       105    
                                                                                                               90          103      

   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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 13)

Asymmetric Unit(hide GO term definitions)
Chain H,I,J,K   (HVM07_MOUSE | P01751)
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: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.

Chain L,M,N,O   (LV1B_MOUSE | P01724)
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.

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

UniProtKB/Swiss-Prot
        HVM07_MOUSE | P017511a6u 1a6v 1a6w 1ngp 1ngq 1nqb 1oaq 1oar 1oax 1oay 1oaz 1ocw 2bjm
        LV1B_MOUSE | P017241a6u 1a6v 1a6w 1dl7 1oaq 1oar 1oax 1oay 1oaz 1ocw 1q0y 2bjm

(-) Related Entries Specified in the PDB File

1oaq FREE CONFORMATION AB1 OF THE IGE SPE-7
1oar FV IGE SPE-7 IN COMPLEX WITH ALIZARIN RED
1oax FV STRUCTURE OF THE IGE SPE-7 IN COMPLEX WITH ACENAPHTHENEQUINONE
1oay ANTIBODY MULTISPECIFICITY MEDIATED BY CONFORMATIONAL DIVERSITY
1oaz IGE FV SPE7 COMPLEXED WITH A RECOMBINANT THIOREDOXIN