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
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SORTASE A FROM STAPHYLOCOCCUS AUREUS
 
Authors :  Y. Zong, T. W. Bice, H. Ton-That, O. Schneewind, S. V. Narayana
Date :  22 Apr 04  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Sortase, Beta Barrel, Transpeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zong, T. W. Bice, H. Ton-That, O. Schneewind, S. V. Narayana
Crystal Structures Of Staphylococcus Aureus Sortase A And Its Substrate Complex
J. Biol. Chem. V. 279 31383 2004
PubMed-ID: 15117963  |  Reference-DOI: 10.1074/JBC.M401374200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SORTASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: NOVAGEN PET 15B
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DELTA-N59 (RESIDUES 61-206)
    Gene: SRT
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1T2P)

(-) Sites  (0, 0)

(no "Site" information available for 1T2P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T2P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:90 -Pro A:91
2Gly B:90 -Pro B:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T2P)

(-) Exons   (0, 0)

(no "Exon" information available for 1T2P)

(-) 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:145
 aligned with Q9S446_STAAU | Q9S446 from UniProtKB/TrEMBL  Length:206

    Alignment length:145
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201     
         Q9S446_STAAU    62 KPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
               SCOP domains d1t2pa_ A: Sortase A                                                                                                                              SCOP domains
               CATH domains 1t2pA00 A:62-206  [code=2.40.260.10, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeehhhheeeeee....hhhhhhhheee..........eeeeeee...........hhhhh....eeeeee..eeeeeeeeeeeeehhhhh...........eeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t2p A  62 KPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201     


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with Q9S446_STAAU | Q9S446 from UniProtKB/TrEMBL  Length:206

    Alignment length:146
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         Q9S446_STAAU    61 AKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
               SCOP domains d1t2pb_ B: Sortase A                                                                                                                               SCOP domains
               CATH domains 1t2pB00 B:61-206  [code=2.40.260.10, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeehhhheeeeee....hhhhhh..eee..........eeeeeee...........hhhhh....eeeeee..eeeeeee............--------..eeeeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t2p B  61 AKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVG--------DKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
                                    70        80        90       100       110       120       130       140       150       160      |  -     | 180       190       200      
                                                                                                                                    167      176                              


Chain C from PDB  Type:PROTEIN  Length:145
 aligned with Q9S446_STAAU | Q9S446 from UniProtKB/TrEMBL  Length:206

    Alignment length:145
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201     
         Q9S446_STAAU    62 KPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
               SCOP domains d1t2pc_ C: Sortase A                                                                                                                              SCOP domains
               CATH domains 1t2pC00 C:62-206  [code=2.40.260.10, no name defined]                                                                                             CATH domains
           Pfam domains (1) --------------Sortase-1t2pC01 C:76-205                                                                                                          - Pfam domains (1)
           Pfam domains (2) --------------Sortase-1t2pC02 C:76-205                                                                                                          - Pfam domains (2)
           Pfam domains (3) --------------Sortase-1t2pC03 C:76-205                                                                                                          - Pfam domains (3)
         Sec.struct. author ............eeeeehhhheeeee.....hhhhhhhh.ee..........eeeeeee...........hhhhh....eeeee....eeeeee......hhhhh...........eeeeeeeeeee....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t2p C  62 KPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSIRDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK 206
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sortase] (11)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9S446_STAAU | Q9S446)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
(no "Ligands, Modified Residues, Ions" information available for 1t2p)
 
  Sites
(no "Sites" information available for 1t2p)
 
  Cis Peptide Bonds
    Gly A:90 - Pro A:91   [ RasMol ]  
    Gly B:90 - Pro B:91   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  1t2p
    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
  Q9S446_STAAU | Q9S446
    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
  Q9S446_STAAU | Q9S446
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9S446_STAAU | Q9S446: 1ija 1t2o 1t2w 2kid

(-) Related Entries Specified in the PDB File

1t2o NATIVE CRYSTAL
1t2w SAME PROTEIN COMPLEXED WITH LPETG PEPTIDE