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 :  CRYSTAL STRUCTURE OF S. AUREUS AUTOLYSIN E
 
Authors :  M. Mihelic, M. Renko, A. Dobersek, L. Bedrac, D. Turk
Date :  08 May 14  (Deposition) - 14 Oct 15  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Autolysin, Glycosidase, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mihelic, K. Vlahovicek-Kahlina, M. Renko, S. Mesnage, A. Dobersek A. Taler-Vercic, A. Jakas, D. Turk
The Mechanism Behind The Selection Of Two Different Cleavag Sites In Nag-Nam Polymers
Iucrj V. 4 185 2017
PubMed: search  |  Reference-DOI: 10.1107/S2052252517000367

(-) Compounds

Molecule 1 - AUTOLYSIN E
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 35-258
    Gene: SAV2307
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50 / ATCC 700699

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:256 , TYR A:257binding site for residue CL A 301
2AC2SOFTWAREASN A:204 , ASN A:215 , HOH A:434 , HOH A:618binding site for residue CL A 302
3AC3SOFTWAREGLY A:106 , GLY A:108 , LYS A:143 , LYS A:243 , HOH A:472 , HOH A:508binding site for residue CL A 303
4AC4SOFTWAREGLY A:164 , ALA A:165 , LYS A:175 , TYR A:177binding site for residue CL A 304
5AC5SOFTWAREGLU A:145binding site for residue CL A 305
6AC6SOFTWAREPRO A:94 , LYS A:248 , HOH A:585 , HOH A:590binding site for residue CL A 306
7AC7SOFTWARESER A:96 , GLU A:97 , SER A:98 , ASN A:218 , HOH A:407 , HOH A:504binding site for residue CL A 307
8AC8SOFTWAREALA A:74 , LYS A:85 , TRP A:214binding site for residue CL A 308
9AC9SOFTWAREASN A:101 , ASN A:112 , GLY A:114 , LYS A:115 , HOH A:491 , HOH A:492binding site for residue CL A 309

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PIA)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh......eeee..eeee.hhhhhhhhhh....hhhhh........hhhhhhhhhh.hhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhheee..eee.........hhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pia A  32 AAANDVNYSFDEAVSMQQGKGIVQTKEEDGKFVEANNNEIAKAMTISDNDMKYMDITEKVPMSESEVNQLLKGKGILENRGKVFLEAQEKYEVNVIYLVSHALVETGNGKSELAKGIKDGKKRYYNFFGIGAFDSSAVRSGKSYAEKEQWTSPDKAIIGGAKFIRNEYFENNQLNLYQMRWNPENPAQHQYASDIRWADKIAKLMDKSYKQFGIKKDDIRQTYYK 258
                                    41        51        61        71      ||83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253     
                                                                         78|                                                                                                                                                                                 
                                                                          81
   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 4PIA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PIA)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4pia)
 

(-) 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
  4pia
    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
  A0A0H3JT72_S | A0A0H3JT72
    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
  A0A0H3JT72_S | A0A0H3JT72
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H3JT72_S | A0A0H3JT72: 4pi7 4pi8 4pi9

(-) Related Entries Specified in the PDB File

4pi7 4pi8 4pi9