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(-) Description

Title :  ENGINEERING THE SPECIES-SPECIFICITY OF AN INHIBITORY ANTIBODY TARGETING A MODULATOR OF TUMOR STROMA
 
Authors :  I. Grossman, D. Fass
Date :  17 Aug 15  (Deposition) - 10 Feb 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Enzyme, Disulfide Bonds, Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Grossman, T. Ilani, S. J. Fleishman, D. Fass
Overcoming A Species-Specificity Barrier In Development Of An Inhibitory Antibody Targeting A Modulator Of Tumor Stroma.
Protein Eng. Des. Sel. V. 29 135 2016
PubMed-ID: 26819240  |  Reference-DOI: 10.1093/PROTEIN/GZV067

(-) Compounds

Molecule 1 - SULFHYDRYL OXIDASE 1
    Chains: A, B
    EC Number: 1.8.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 36-275
    Gene: QSOX1, QSCN6, SOX
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFA SWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATL P GAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVT LDL SQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTRD
    Synonym: MSOX,QUIESCIN Q6,SKIN SULFHYDRYL OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5D8I)

(-) Sites  (0, 0)

(no "Site" information available for 5D8I)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:73 -A:76
2A:104 -A:113
3B:73 -B:76
4B:104 -B:113

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Asp A:43 -Pro A:44
2Arg A:94 -Pro A:95
3Phe A:121 -Pro A:122
4Phe A:237 -Pro A:238
5Arg B:94 -Pro B:95
6Phe B:121 -Pro B:122
7Phe B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D8I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D8I)

(-) Exons   (0, 0)

(no "Exon" information available for 5D8I)

(-) 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 A from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...hhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......eeeee.........ee......hhhhhhhhhhhhhhhh..............hhhhhhhhhhhh...eeeeeee....hhhhhhhhhh.....eeeeeee..hhhhhhhh......eeeeee....eee......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8i A  38 LYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFASWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLPGAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDLSQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTR 274
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee...hhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......eeeee.........eee.....hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh...eeeeeee....hhhhhhhhhh.....eeeeeee..hhhhhhhh......eeeeee....eee......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8i B  37 VLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFASWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLPGAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDLSQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTR 274
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
   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  (0, 0)

(no "SCOP Domain" information available for 5D8I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D8I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D8I)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:94 - Pro A:95   [ RasMol ]  
    Arg B:94 - Pro B:95   [ RasMol ]  
    Asp A:43 - Pro A:44   [ RasMol ]  
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 Related Entries

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        QSOX1_MOUSE | Q8BND5: 3t58 3t59 5d93 5d96

(-) Related Entries Specified in the PDB File

3q6o 3Q6O IS THE HUMAN ORTHOLOG