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(-) Description

Title :  TRASTUZUMAB FAB COMPLEXED WITH PROTEIN L AND PROTEIN A FRAGMENTS
 
Authors :  K. N. Avery, C. Zer, K. P. Bzymek, J. C. Williams
Date :  15 Oct 12  (Deposition) - 09 Oct 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B,E,H
Keywords :  Monoclonal Antibody, Immune System, Cancer Therapeutic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Donaldson, C. Zer, K. N. Avery, K. P. Bzymek, D. A. Horne, J. C. Williams
Identification And Grafting Of A Unique Peptide-Binding Sit In The Fab Framework Of Monoclonal Antibodies.
Proc. Natl. Acad. Sci. Usa V. 110 17456 2013
PubMed-ID: 24101516  |  Reference-DOI: 10.1073/PNAS.1307309110

(-) Compounds

Molecule 1 - TRASTUZUMAB LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - TRASTUZUMAB HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - IMMUNOGLOBULIN G-BINDING PROTEIN A
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SPA, SAV0111
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50 / ATCC 700699
    Synonym: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A
 
Molecule 4 - PROTEIN L FRAGMENT
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: FINEGOLDIA MAGNA
    Organism Taxid: 1260

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:59 , TYR B:60 , LYS B:65BINDING SITE FOR RESIDUE CL B 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:96
4B:147 -B:203

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:153 -Pro B:154
5Glu B:155 -Pro B:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HKZ)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d4hkza1 A:1-107 automated matches                                                                          d4hkza2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkz A   1 DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeehhhhh....ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkz B   1 EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain E from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains d4hkze_ E: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeeehhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4hkz E  19 SEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMNIKFAG  81
                                    28        38        48        58        68        78   


Chain H from PDB  Type:PROTEIN  Length:54
                                                                                      
               SCOP domains d4hkzh_ H: automated matches                           SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 4hkz H   1 GSYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA  54
                                    10        20        30        40        50
   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 alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hkz
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPA_STAAM | P0A015: 4hjg 4ioi
UniProtKB/TrEMBL
        Q51918_FINMA | Q51918: 1hez 1ymh 1ynt 2fs1 4hjg 4ioi

(-) Related Entries Specified in the PDB File

1n8z 4hjg