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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  RETROFITTING ANTIBODIES WITH STABILIZING MUTATIONS. HERCEPTIN SCFV MUTANT K30D/S52D.
 
Authors :  D. B. Langley, B. Roome, D. Christ
Date :  04 Dec 14  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Antibody Stabilization Mutations, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. B. Langley, B. Roome, D. Christ
Retrofitting Antibodies With Stabilizing Mutations
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HUMAN VARIABLE HEAVY CHAIN OF HERCEPTIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HUMAN VARIABLE LIGHT CHAIN OF HERCEPTIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4X4Y)

(-) Sites  (0, 0)

(no "Site" information available for 4X4Y)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2B:23 -B:88
3C:22 -C:96
4D:23 -D:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser B:7 -Pro B:8
2Gly B:68 -Thr B:69
3Thr B:69 -Asp B:70
4Thr B:94 -Pro B:95
5Ser D:7 -Pro D:8
6Thr D:94 -Pro D:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4X4Y)

(-) 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 A from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.hhhh..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4y A   1 EVQLVESGGGLVQPGGSLRLSCAASGFNIDDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDVWGQGTLVTVS 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee......eeeee...ee.......eeee.....eeeee...hhhhheeeeeee......ee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4x4y B   1 DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSADFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEI 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4x4y C   2 VQLVESGGGLVQPGGSLRLSCAASGFNIDDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWYAMDVWGQGTLVTVS 119
                                    11        21        31        41        51        61        71        81        91       106       116   
                                                                                                                            99|              
                                                                                                                            105              


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee.......eeeeee.....eeeeee...ee..eee....eeeee...hhhhheeeeeee......ee...eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4x4y D   1 DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSADFLYSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVE 105
                                    10        20        30        40        50    ||  67        77        87        97        
                                                                                 55|                                          
                                                                                  63
   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 4X4Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X4Y)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4x4y)
 
  Cis Peptide Bonds
    Gly B:68 - Thr B:69   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Ser D:7 - Pro D:8   [ RasMol ]  
    Thr B:69 - Asp B:70   [ RasMol ]  
    Thr B:94 - Pro B:95   [ RasMol ]  
    Thr D:94 - Pro D:95   [ RasMol ]  
 

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

4x4x 4x4z