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 :  1.82 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF HOLO-(ACYL-CARRIER-PROTEIN) SYNTHASE (ACPS) FROM STAPHYLOCOCCUS AUREUS
 
Authors :  A. S. Halavaty, G. Minasov, L. Shuvalova, I Dubrovska, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  13 Mar 13  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Holo-(Acyl-Carrier-Protein) Synthase, Structural Genomics, Infectious Deseases, Fatty Acid Biosynthesis, Lipid Synthesis, Magnesium, Metal-Binding, Transferase, Center For Structural Genomics Of Infectious Diseases, Csgid, Niaid, National Institute Of Allergy And Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, Y. Kim, G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, M. Zhou, O. Onopriyenko, T. Skarina, L. Papazisi, K. Kwon, S. N. Peterson, A. Joachimiak, A. Savchenko, W. F. Anderson
Structural Characterization And Comparison Of Three Acyl-Carrier-Protein Synthases From Pathogenic Bacteria.
Acta Crystallogr. , Sect. D V. 68 1359 2012
PubMed-ID: 22993090  |  Reference-DOI: 10.1107/S0907444912029101

(-) Compounds

Molecule 1 - HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE
    Chains: A, B, C
    EC Number: 2.7.8.7
    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: ACYL-CARRIER-PROTEIN SYNTHASE
    Gene: ACPS, SACOL2061
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: HOLO-ACP SYNTHASE, 4'-PHOSPHOPANTETHEINYL TRANSFERASE ACPS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4JM7)

(-) Sites  (0, 0)

(no "Site" information available for 4JM7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JM7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JM7)

(-) 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:122
                                                                                                                                                          
               SCOP domains d4jm7a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...eeeeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eee...eee....eeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jm7 A -12 DLGTENLYFQSNAMIHGIGVDLIEIDRIQALYSKQPKLVERILTKNEQHKFNNFTHEQRKIEFLAGRFATKEAFSKALGVAFNDIDCYNDGKPKIDYEGFIVHVSISHTEHYAMSQVVLEKS 117
                                    -3         7        17        27        37        47        57        73        83|       95       105       115  
                                                                                                         66|        83|                               
                                                                                                          73         86                               


Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains d4jm7b_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..ee....ee.....eeeeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4jm7 B  -3 QSNAMIHGIGVDLIEIDRIQALYSKQPKLVERILTKNEQHKFNNFTHEQRKIEFLAGRFATKEAFSKALGVAFNDIDCYNDLGKPKIDYEGFIVHVSISHTEHYAMSQVVLEKSAF 119
                                     6        16        26        36        46        56        66|       82||      93       103       113      
                                                                                                66|        83|                                  
                                                                                                 73         85                                  


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4jm7c_ C: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee.....eeeeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jm7 C  -2 SNAMIHGIGVDLIEIDRIQALYSKQPKLVERILTKNEQHKFNNFTHEQRKIEFLAGRFATKEAFSKALGTGLGKHVAFNDIDCYNDELGKPKIDYEGFIVHVSISHTEHYAMSQVVLEKSAF 119
                                     7        17        27        37        47        57        67        77        87        97       107       117
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JM7)

(-) Gene Ontology  (8, 8)

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 4jm7)
 
  Sites
(no "Sites" information available for 4jm7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jm7)
 

(-) 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
  4jm7
    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
  ACPS_STAAC | Q5HED0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.8.7
    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
  ACPS_STAAC | Q5HED0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ACPS_STAAC | Q5HED0: 4dxe 5cxd

(-) Related Entries Specified in the PDB File

3f09 1.82 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF HOLO-(ACYL- CARRIER-PROTEIN) SYNTHASE (ACPS) FROM STAPHYLOCOCCUS AUREUS RELATED ID: CSGID-IDP00816 RELATED DB: TARGETTRACK