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(-) Description

Title :  PROTEIN A BINDING BY AN ENGINEERED AFFIBODY MOLECULE
 
Authors :  T. Hard
Date :  19 Feb 13  (Deposition) - 21 Aug 13  (Release) - 16 Oct 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Binding Protein, Protein Engineering, Protein A, Z Domain, Affibody Molecule, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Lindborg, A. Dubnovitsky, K. Olesen, T. Bjorkman, L. Abrahmsen, J. Feldwisch, T. Hard
High-Affinity Binding To Staphylococcal Protein A By An Engineered Dimeric Affibody Molecule.
Protein Eng. Des. Sel. V. 26 635 2013
PubMed-ID: 23924760  |  Reference-DOI: 10.1093/PROTEIN/GZT038

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN G-BINDING PROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SPA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: IN-HOUSE STANDARD EXPRESSION VECTOR WITH T7 PROMOTER
    Synonym: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A
 
Molecule 2 - ZPA963
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
    Other Details: IN-HOUSE STANDARD EXPRESSION VECTOR WITH T7 PROMOTER

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M5A)

(-) Sites  (0, 0)

(no "Site" information available for 2M5A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M5A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M5A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

NMR Structure
   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:58
 aligned with SPA_STAAU | P38507 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:58
                                   221       231       241       251       261        
            SPA_STAAU   212 ADNKFNKEQQNAFYEILHLPNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAPK 269
               SCOP domains d2m5aa_ A: Immunoglobulin-binding protein A modules        SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2m5a A   1 VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK  58
                                    10        20        30        40        50        


Chain B from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains d2m5ab_ B: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2m5a B 101 VDNKFNKETQEASWEIFTLPNLNGRQVAAFISSLLDDPSQSANLLAEAKKLNDAQAPK 158
                                   110       120       130       140       150
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5A)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (SPA_STAAU | P38507)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
    GO:0019865    immunoglobulin binding    Interacting selectively and non-covalently with an immunoglobulin.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPA_STAAU | P38507: 1bdc 1bdd 1edi 1edj 1edk 1edl 1fc2 1h0t 1lp1 1q2n 1ss1 2jwd 2spz 3mzw 4npd 4npe 4npf 4wwi 4y4y 4y5z 4zmd 4znc 5cbn 5cbo 5coc 5ewx 5h75 5h76 5h77 5h79 5h7a 5h7b 5h7c 5h7d 5x3f 5xby

(-) Related Entries Specified in the PDB File

1h0t RELATED ID: 19043 RELATED DB: BMRB