Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF CATALYTIC DOMAIN OF ENDOLYSIN FROM CLOSTRIDIUM PERFRINGENS PHAGE PHISM101
 
Authors :  S. Kamitori, H. Yoshida
Date :  17 May 13  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta/Alpha Barrel, Muramidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Tamai, H. Yoshida, H. Sekiya, H. Nariya, S. Miyata, A. Okabe, T. Kuwahara, J. Maki, S. Kamitori
X-Ray Structure Of A Novel Endolysin Encoded By Episomal Phage Phism101 Of Clostridium Perfringens
Mol. Microbiol. 2014
PubMed: search  |  Reference-DOI: 10.1111/MMI.12559

(-) Compounds

Molecule 1 - AUTOLYTIC LYSOZYME
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD II
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-218
    Gene: CPR_C0050
    Organism Scientific: CLOSTRIDIUM PHAGE PHISM101
    Organism Taxid: 396359
    Strain: SM101

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:-3 , ASP A:13 , TYR A:66 , ASP A:101 , GLU A:103 , TYR A:135 , GLN A:177 , ASP A:192 , HOH A:669 , HOH A:873 , HOH A:931BINDING SITE FOR RESIDUE NDG A 501
2AC2SOFTWAREGLY A:60 , SER A:62 , ASP A:95 , GLU A:198 , PHE A:201 , HOH A:687 , HOH A:740 , HOH A:760 , HOH A:910BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREHIS A:-2 , HIS A:-6 , HIS A:-5 , HIS A:-4 , VAL A:-7 , HOH A:738 , HOH A:858 , HOH A:904BINDING SITE FOR RESIDUE PO4 A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KRU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KRU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KRU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KRU)

(-) Exons   (0, 0)

(no "Exon" information available for 4KRU)

(-) Sequences/Alignments

Asymmetric/Biological 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeehhhhh..hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh........eeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh.eeee.................eeeeeeee........eeeeee.hhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kru A  -7 VHHHHHHMQSRNNNNLKGIDVSNWKGNINFESVKNDGVEVVYIKATEGNYFKDKYAKQNYEGAKEQGLSVGFYHFFRANKGAKDQANFFIDYLNEIGAVNYDCKLALDIETTEGVGVRDLTSMCIEFLEEVKRLTGKEVVVYTYTSFANNNLDSRLGNYPVWIAHYGVNTPGANNIWSSWVGFQYSENGSVAGVNGGCDMNEFTEEIFIDSSNF 207
                                  || 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
                                 -1|                                                                                                                                                                                                              
                                   1
   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 4KRU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KRU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KRU)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4kru)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4kru
    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
  Q0SPG7_9CAUD | Q0SPG7
    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)
  3.2.1.17
    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
  Q0SPG7_9CAUD | Q0SPG7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q0SPG7_9CAUD | Q0SPG7: 4krt

(-) Related Entries Specified in the PDB File

4krt X-RAY STRUCTURE OF ENDOLYSIN INCLUDING SH3 DOMAINS