Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF GB1 WITH LBT PROBE
 
Authors :  T. Saio, K. Ogura, M. Yokochi, Y. Kobashigawa, F. Inagaki
Date :  28 Oct 08  (Deposition) - 15 Sep 09  (Release) - 15 Sep 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lanthanide Binding Peptide, Gb1, Lbt, Paramagnetic Effect, Olivia, Cell Wall, Igg-Binding Protein, Peptidoglycan- Anchor, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Saio, K. Ogura, M. Yokochi, Y. Kobashigawa, F. Inagaki
Two-Point Anchoring Of A Lanthanide-Binding Peptide To A Target Protein Enhances The Paramagnetic Anisotropic Effect
J. Biomol. Nmr V. 44 157 2009
PubMed-ID: 19468839  |  Reference-DOI: 10.1007/S10858-009-9325-Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN G-BINDING PROTEIN G
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PETDUET
    Expression System Vector Type: VECTOR
    Fragment: L2GB
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS SP. GROUP G
    Organism Taxid: 1320
    Synonym: IGG-BINDING PROTEIN G

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1LA1Ligand/IonLANTHANUM (III) ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:3 , ASP A:4 , THR A:5 , ASN A:7 , ASP A:8BINDING SITE FOR RESIDUE LA A 76

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:1 -A:38

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RPV)

(-) Exons   (0, 0)

(no "Exon" information available for 2RPV)

(-) 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:75
 aligned with SPG1_STRSG | P06654 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:86
                                   206       216       226       236       246       256       266       276      
           SPG1_STRSG   197 DYHKNLINNAKTVEGVKELIDEILAALPKTDTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE 282
               SCOP domains d2rp  va_ A: au     to    mated matches                                                SCOP domains
               CATH domains 2rpv  A00 A:1-7     5      [code=3.10.20.10, no name defined]                          CATH domains
               Pfam domains --------------------------------IgG_binding_B-2rpvA01 A:22-75                          Pfam domains
         Sec.struct. author ....--........h-----hh----hh..eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhh...eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2rpv A   1 CYVD--TNNDGAYEG-----DE----LSGTMEYKLILNGKTLKGETTTCAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE  75
                               |  |  8    |    -||    | 19        29        39        49        59        69      
                               4  5      13    14|   16                                                           
                                                15
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: IgG_binding_B] (24)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (SPG1_STRSG | P06654)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    LA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rpv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rpv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPG1_STRSG | P06654
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SPG1_STRSG | P06654
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPG1_STRSG | P06654: 1em7 1gb1 1igc 1igd 1le3 1mpe 1mvk 1pga 1pgb 1pgx 1pn5 1q10 2cwb 2den 2gb1 2igd 2igh 2j52 2j53 2ju6 2k0p 2kbt 2klk 2lgi 2mbb 2n7j 2nmq 2plp 2rmm 3gb1 3mp9 4kgr 4kgs 4kgt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RPV)