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(-) Description

Title :  PROTEIN Z IN COMPLEX WITH AN IN VITRO SELECTED AFFIBODY
 
Authors :  M. Hogbom, M. Eklund, P. A. Nygren, P. Nordlund
Date :  07 May 02  (Deposition) - 18 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  In Vitro Evolved, Protein-Protein Complex, Three-Helix Bundle, Affibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hogbom, M. Eklund, P. A. Nygren, P. Nordlund
Structural Basis For Recognition By An In Vitro Evolved Affibody.
Proc. Natl. Acad. Sci. Usa V. 100 3191 2003
PubMed-ID: 12604795  |  Reference-DOI: 10.1073/PNAS.0436100100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AFFIBODY BINDING PROTEIN Z
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: IN VITRO SELECTED BINDING PROTEIN
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
 
Molecule 2 - IMMUNOGLOBULIN G BINDING PROTEIN A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 2-58
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO48Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , HOH A:317 , HOH A:322 , HOH A:386 , ARG B:27BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREASN B:23 , GLU B:24 , SO4 B:303 , MG B:401 , HOH B:439BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWAREASP A:36 , HOH A:336 , ASN B:6 , GLN B:10 , GLU B:25 , SO4 B:302 , MG B:401 , HOH B:414 , HOH B:444BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWAREASN A:23 , ASP A:24 , PRO A:25 , HOH A:340 , HOH A:403BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREASN B:23 , GLU B:25 , SO4 B:302 , SO4 B:303BINDING SITE FOR RESIDUE MG B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LP1)

(-) Exons   (0, 0)

(no "Exon" information available for 1LP1)

(-) 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:55
                                                                                       
               SCOP domains d1lp1a_ A: Immunoglobulin-binding protein A modules     SCOP domains
               CATH domains 1lp1A00 A:4-58 Immunoglobulin FC, subunit C             CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 1lp1 A   4 KFNKELSVAGREIVTLPNLNDPQKKAFIFSLWDDPSQSANLLAEAKKLNDAQAPK  58
                                    13        23        33        43        53     


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with SPA_STAAU | P38507 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:54
                                   224       234       244       254       264    
            SPA_STAAU   215 KFNKEQQNAFYEILHLPNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAP 268
               SCOP domains d1lp1b_ B: Immunoglobulin-binding protein A modules    SCOP domains
               CATH domains 1lp1B00 B:4-57 Immunoglobulin FC, subunit C            CATH domains
               Pfam domains B-1lp1B01 B:4-54                                   --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 1lp1 B   4 KFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAP  57
                                    13        23        33        43        53
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: B] (6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain B   (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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  1lp1
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  SPA_STAAU | P38507
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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 1q2n 1ss1 2jwd 2m5a 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

2spz NMR STRUCTURE OF PROTEIN Z, ONE OF THE PROTEINS IN THE COMPLEX