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 :  2.1 ANGSTROM CRYSTAL STRUCTURE OF 3-OXOACYL-(ACYL-CARRIER-PROTEIN) SYNTHASE III
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  31 Mar 09  (Deposition) - 28 Apr 09  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acyl Carrier Protein, Fabh, Structural Genomics, Transferase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - 3-OXOACYL-(ACYL-CARRIER-PROTEIN) SYNTHASE III
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABH, BURPS1710B_0096
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3GWE)

(-) Sites  (0, 0)

(no "Site" information available for 3GWE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GWE)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:95 -Pro A:96
2Gly A:186 -Pro A:187
3Gly A:334 -Tyr A:335
4Leu B:95 -Pro B:96
5Gly B:186 -Pro B:187
6Gly B:334 -Tyr B:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GWE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GWE)

(-) Exons   (0, 0)

(no "Exon" information available for 3GWE)

(-) 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:341
 aligned with Q3JY40_BURP1 | Q3JY40 from UniProtKB/TrEMBL  Length:344

    Alignment length:341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
         Q3JY40_BURP1     4 AAHPPRAAIADIAGHLPEQVLTNDVLAQLYPDWPAEKILAKTGIRERRIAAPRETAADLAYEAARKLFAQGAVGADQVDFVILCTQAPDYVLPTSACMLQHRLGIPTHAGALDVNLGCSGYVYGLSLAKGLVETGAARCVLLLTADTYSKYLHPLDKSVRTLFGDGASATAVIAEHGELERIGPFVFGTDGRGAPNLIVKAGLFREPKSADSAREHEDASGNVRTDEHLYMNGAEVMAFSLAEVPRAADRLLALAGEPRENIDCFVLHQANRFMLDALRKKMKIPEHKFPVLMEHCGNTVSSTLPLALETMRANGTLARGMRLMLLGFGVGYSWAGCLVNF 344
               SCOP domains d3gwea1 A:4-184 automated matches                                                                                                                                                    d3gwea2 A:185-344 automated matches                                                                                                                              SCOP domains
               CATH domains 3gweA01 A:4-183  [code=3.40.47.10, no name defined]                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeehhhhhhhh...hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh..hhhhh.eeeeee........hhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeeee.....eeeeeeee.hhhhh.eee..........hhhhh.ee.....ee....eeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwe A   4 AAHPPRAAIADIAGHLPEQVLTNDVLAQLYPDWPAEKILAKTGIRERRIAAPRETAADLAYEAARKLFAQGAVGADQVDFVILCTQAPDYVLPTSACMLQHRLGIPTHAGALDVNLGCSGYVYGLSLAKGLVETGAARCVLLLTADTYSKYLHPLDKSVRTLFGDGASATAVIAEHGELERIGPFVFGTDGRGAPNLIVKAGLFREPKSADSAREHEDASGNVRTDEHLYMNGAEVMAFSLAEVPRAADRLLALAGEPRENIDCFVLHQANRFMLDALRKKMKIPEHKFPVLMEHCGNTVSSTLPLALETMRANGTLARGMRLMLLGFGVGYSWAGCLVNF 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with Q3JY40_BURP1 | Q3JY40 from UniProtKB/TrEMBL  Length:344

    Alignment length:337
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       
         Q3JY40_BURP1     8 PRAAIADIAGHLPEQVLTNDVLAQLYPDWPAEKILAKTGIRERRIAAPRETAADLAYEAARKLFAQGAVGADQVDFVILCTQAPDYVLPTSACMLQHRLGIPTHAGALDVNLGCSGYVYGLSLAKGLVETGAARCVLLLTADTYSKYLHPLDKSVRTLFGDGASATAVIAEHGELERIGPFVFGTDGRGAPNLIVKAGLFREPKSADSAREHEDASGNVRTDEHLYMNGAEVMAFSLAEVPRAADRLLALAGEPRENIDCFVLHQANRFMLDALRKKMKIPEHKFPVLMEHCGNTVSSTLPLALETMRANGTLARGMRLMLLGFGVGYSWAGCLVNF 344
               SCOP domains d3gweb1 B:8-184 automated matches                                                                                                                                                d3gweb2 B:185-344 automated matches                                                                                                                              SCOP domains
               CATH domains 3gweB01 B:8-183  [code=3.40.47.10, no name defined]                                                                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee...eeeehhhhhhhh...hhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....hhhhh.eeeeee........hhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeee......eeeeeeee.hhhhh.eee................ee.....ee....eeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee...hhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwe B   8 PRAAIADIAGHLPEQVLTNDVLAQLYPDWPAEKILAKTGIRERRIAAPRETAADLAYEAARKLFAQGAVGADQVDFVILCTQAPDYVLPTSACMLQHRLGIPTHAGALDVNLGCSGYVYGLSLAKGLVETGAARCVLLLTADTYSKYLHPLDKSVRTLFGDGASATAVIAEHGELERIGPFVFGTDGRGAPNLIVKAGLFREPKSADSAREHEDASGNVRTDEHLYMNGAEVMAFSLAEVPRAADRLLALAGEPRENIDCFVLHQANRFMLDALRKKMKIPEHKFPVLMEHCGNTVSSTLPLALETMRANGTLARGMRLMLLGFGVGYSWAGCLVNF 344
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GWE)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3JY40_BURP1 | Q3JY40)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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 3gwe)
 
  Sites
(no "Sites" information available for 3gwe)
 
  Cis Peptide Bonds
    Gly A:186 - Pro A:187   [ RasMol ]  
    Gly A:334 - Tyr A:335   [ RasMol ]  
    Gly B:186 - Pro B:187   [ RasMol ]  
    Gly B:334 - Tyr B:335   [ RasMol ]  
    Leu A:95 - Pro A:96   [ RasMol ]  
    Leu B:95 - Pro B:96   [ RasMol ]  
 

(-) 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
  3gwe
    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
  Q3JY40_BURP1 | Q3JY40
    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
  Q3JY40_BURP1 | Q3JY40
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q3JY40_BURP1 | Q3JY40: 3gwa

(-) Related Entries Specified in the PDB File

3gwa 1.6 ANGSTROM CRYSTAL STRUCTURE OF 3-OXOACYL-(ACYL-CARRIER-2 PROTEIN) SYNTHASE III RELATED ID: BUPSA.00171.A RELATED DB: TARGETDB