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 - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE PLYG CELL WALL BINDING DOMAIN
 
Authors :  B. F. Volkman, J. S. Dias, F. C. Peterson
Date :  01 Oct 10  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Bacillus Anthracis Gamma- Phage Endolysin, Plyg, Cell Wall Binding Domain, Homodimer, Act-Type Domain, Carbohydrate-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Dias, F. C. Peterson, B. F. Volkman
Tbd
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N-ACETYLMURAMOYL-L-ALANINE AMIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21[PREP4]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CELL WALL BINDING DOMAIN, RESIDUES 151-233
    Gene: GAMMALSU_0017, GAMMAUSAM_0017, PLYG
    Organism Scientific: BACILLUS PHAGE GAMMA
    Organism Taxid: 347962

 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 2L48)

(-) Sites  (0, 0)

(no "Site" information available for 2L48)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L48)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L48)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2L48)

(-) Exons   (0, 0)

(no "Exon" information available for 2L48)

(-) 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:85
 aligned with Q8LTE6_9CAUD | Q8LTE6 from UniProtKB/TrEMBL  Length:233

    Alignment length:86
                                   157       167       177       187       197       207       217       227      
         Q8LTE6_9CAUD   148 GAFIQKVKNGNVATTSPTKQNIIQSGAFSPYETPDVMGALTSLKMTADFILQSDGLTYFISKPTSDAQLKAMKEYLDRKGWWYEVK 233
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-..................eeee......hhhhhhhhhhhh...eeeee.....eeeee...hhhhhhhhhhhhhhh...eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2l48 A 149 GS-IQKVKNGNVATTSPTKQNIIQSGAFSPYETPDVMGALTSLKMTADFILQSDGLTYFISKPTSDAQLKAMKEYLDRKGWWYEVK 233
                             | |   157       167       177       187       197       207       217       227      
                             | |                                                                                  
                           150 |                                                                                  
                             151                                                                                  


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q8LTE6_9CAUD | Q8LTE6 from UniProtKB/TrEMBL  Length:233

    Alignment length:86
                                   157       167       177       187       197       207       217       227      
         Q8LTE6_9CAUD   148 GAFIQKVKNGNVATTSPTKQNIIQSGAFSPYETPDVMGALTSLKMTADFILQSDGLTYFISKPTSDAQLKAMKEYLDRKGWWYEVK 233
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-...................eee...hhhhhhhhhhhhhhh...eeeee.....eeeee...hhhhhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2l48 B 349 GS-IQKVKNGNVATTSPTKQNIIQSGAFSPYETPDVMGALTSLKMTADFILQSDGLTYFISKPTSDAQLKAMKEYLDRKGWWYEVK 433
                             | |   357       367       377       387       397       407       417       427      
                           350 |                                                                                  
                             351
   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 2L48)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L48)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L48)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A,B   (Q8LTE6_9CAUD | Q8LTE6)
molecular function
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0044659    cytolysis by virus of host cell    The killing by a virus of a cell in its host organism by means of the rupture of cell membranes and the loss of cytoplasm.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

 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
(no "Ligands, Modified Residues, Ions" information available for 2l48)
 
  Sites
(no "Sites" information available for 2l48)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2l48)
 

(-) 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 - 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
  2l48
    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
  Q8LTE6_9CAUD | Q8LTE6
    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
  Q8LTE6_9CAUD | Q8LTE6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8LTE6_9CAUD | Q8LTE6: 2l47

(-) Related Entries Specified in the PDB File

2l47