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

(-) Description

Title :  STRUCTURE OF CATALYTICALLY ACTIVE SORTASE FROM CLOSTRIDIUM DIFFICILE
 
Authors :  J. -C. Yin, C. -H. Fei, Y. -Y. Hsiao, J. C. Nix, I. -H. Huang, S. Wang
Date :  22 Sep 16  (Deposition) - 04 Jan 17  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Transpeptidase, Cys-His-Arg Catalytic Triad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Yin, C. H. Fei, Y. C. Lo, Y. Y. Hsiao, J. C. Chang, J. C. Nix, Y. Y. Chang, L. W. Yang, I. H. Huang, S. Wang
Structural Insights Into Substrate Recognition By Clostridium Difficile Sortase.
Front Cell Infect Microbiol V. 6 160 2016
PubMed-ID: 27921010  |  Reference-DOI: 10.3389/FCIMB.2016.00160

(-) Compounds

Molecule 1 - PUTATIVE PEPTIDASE C60B, SORTASE B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 28-224
    Gene: CD630_27180
    Organism Scientific: PEPTOCLOSTRIDIUM DIFFICILE (STRAIN 630)
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GYJ)

(-) Sites  (0, 0)

(no "Site" information available for 5GYJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GYJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GYJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GYJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GYJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5GYJ)

(-) 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:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..hhhhh...eeeeeee.....eeeee.....hhhhh............eee..........eeeeee........hhhhhhhhhhhhhhh..eeeeee..eeeeeeeeeeee.......hhhhhhhhhhhhhhh.............eeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gyj A  29 TKYNHDTKISSELQKKEYKKEDLSKINSDFKFWLSVENTNINYPVVQSKDNSYYLDKDFYKKDSISGTLFMDYRNKSIDDKNIIIYGHNMKNKTMFNNLNKFKDADFFKKNNKIKITLNGKEFLYDVFSAYIVLKTNFNNESDYQNYINDITSKSLYKSPIKVNSNDKIVTLSTCRMVIHGRL 224
                                    38        48        58        68        78        88        98       108       118       128       138       148       158  ||   174       184       194       204    || 221   
                                                                                                                                                              161|                                      209|       
                                                                                                                                                               168                                       217
   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 5GYJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GYJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GYJ)

(-) Gene Ontology  (2, 2)

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
(no "Ligands, Modified Residues, Ions" information available for 5gyj)
 
  Sites
(no "Sites" information available for 5gyj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gyj)
 

(-) 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 ](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
  5gyj
    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
  Q183F3_PEPD6 | Q183F3
    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
  Q183F3_PEPD6 | Q183F3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q183F3_PEPD6 | Q183F3: 4ux7

(-) Related Entries Specified in the PDB File

4ux7 THE STRUCTURE OF C. DIFFICILE SORTASE MUTANT WITH CYSTEINE 233 REPLACED WITH ALANINE