Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUCBP DOMAIN OF THE ADHESION PROTEIN PEPE_0118 FROM PEDIOCOCCUS PENTOSACEUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ID PTR41A
 
Authors :  J. Seetharaman, S. Lew, D. Wang, H. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  28 Feb 10  (Deposition) - 07 Apr 10  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Cell Wall, Peptidoglycan-Anchor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, S. Lew, D. Wang, H. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Mucbp Domain Of The Adhesion Protein Pepe_0118 From Pediococcus Pentosaceus. Northeast Structural Genomics Consortium Target Id Ptr41A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADHESION EXOPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEQUENCE DATABASE RESIDUES 796-902
    Gene: PEPE_0118
    Organism Scientific: PEDIOCOCCUS PENTOSACEUS
    Organism Taxid: 278197
    Strain: ATCC 25745 / 183-1W

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LYY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LYY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:101 -Pro A:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LYY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LYY)

(-) Exons   (0, 0)

(no "Exon" information available for 3LYY)

(-) 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:102
 aligned with Q03HU7_PEDPA | Q03HU7 from UniProtKB/TrEMBL  Length:3017

    Alignment length:102
                                   805       815       825       835       845       855       865       875       885       895  
         Q03HU7_PEDPA   796 THATSTETIHYVNEDGDQVFEDGGGKLDFTRTVTIDDVTNEVVEYGEWTPVTDDEFAAVTSPDKDGYTPDTSEVAAQKPDMTDGPDGTVKDVEVTVTYTANP 897
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeeeeeeee..eee......eeee...ee........ee......eee...ee.................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 3lyy A   1 THATSTETIHYVNEDGDQVFEDGGGKLDFTRTVTIDDVTNEVVEYGEWTPVTDDEFAAVTSPDKDGYTPDTSEVAAQKPDmTDGPDGTVKDVEVTVTYTANP 102
                                    10        20        30        40        50        60        70        80|       90       100  
                                                                                                           81-MSE                 


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with Q03HU7_PEDPA | Q03HU7 from UniProtKB/TrEMBL  Length:3017

    Alignment length:100
                                   807       817       827       837       847       857       867       877       887       897
         Q03HU7_PEDPA   798 ATSTETIHYVNEDGDQVFEDGGGKLDFTRTVTIDDVTNEVVEYGEWTPVTDDEFAAVTSPDKDGYTPDTSEVAAQKPDMTDGPDGTVKDVEVTVTYTANP 897
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MucBP-3lyyB01 B:3-102                                                                                Pfam domains (1)
           Pfam domains (2) MucBP-3lyyB02 B:3-102                                                                                Pfam domains (2)
         Sec.struct. author .eeeeeeeeee.........eeeeeeee..eee......eeee...ee........ee......eee...ee.................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3lyy B   3 ATSTETIHYVNEDGDQVFEDGGGKLDFTRTVTIDDVTNEVVEYGEWTPVTDDEFAAVTSPDKDGYTPDTSEVAAQKPDmTDGPDGTVKDVEVTVTYTANP 102
                                    12        22        32        42        52        62        72        82        92       102
                                                                                                         81-MSE
   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 3LYY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LYY)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Gram-pos_anchor (4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LYY)

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3lyy)
 
  Cis Peptide Bonds
    Asn A:101 - Pro A:102   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  3lyy
    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
  Q03HU7_PEDPA | Q03HU7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q03HU7_PEDPA | Q03HU7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q03HU7_PEDPA | Q03HU7: 2kyw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LYY)