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 :  THE CRYSTAL STRUCTURE OF A DOMAIN OF PHENYLACETATE-COENZYME A LIGASE FROM BACTEROIDES VULGATUS ATCC 8482
 
Authors :  K. Tan, R. Wu, G. Cobb, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  07 Jan 10  (Deposition) - 19 Jan 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tan, R. Wu, G. Cobb, A. Joachimiak
The Crystal Structure Of A Domain Of Phenylacetate-Coenzyme A Ligase From Bacteroides Vulgatus Atcc 8482
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHENYLACETATE-COENZYME A LIGASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG19
    Expression System StrainPPK1037
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 327-432
    GeneBACTEROIDES VULGATUS, BVU_1668
    Organism ScientificBACTEROIDES VULGATUS
    Organism Taxid435590
    StrainATCC 8482

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LAX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LAX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LAX)

(-) 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:106
 aligned with A6L0Y5_BACV8 | A6L0Y5 from UniProtKB/TrEMBL  Length:432

    Alignment length:109
                                   333       343       353       363       373       383       393       403       413       423         
         A6L0Y5_BACV8   324 GRSDDMIILKGVNIFPIQIETILLQFKELGSDYLITLETAESNDEMTVEVELSQLFTDDYGRLQALTREITRQLKDEILVTPRVKLVPKGALPKSEGKAVRVKDLRKTF 432
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3laxA00 A:324-432  [code=3.30.300.30, no name defined]                                                        CATH domains
               Pfam domains ---AMP-binding-3laxA01       -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee..eeehhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeee........---...eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3lax A 324 SNADDmIILKGVNIFPIQIETILLQFKELGSDYLITLETAESNDEmTVEVELSQLFTDDYGRLQALTREITRQLKDEILVTPRVKLVPKGALPKS---AVRVKDLRKTF 432
                                 | 333       343       353       363     | 373       383       393       403       413    |  423         
                                 |                                     369-MSE                                          418 422          
                               329-MSE                                                                                                   

   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 3LAX)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ANL (32)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6L0Y5_BACV8 | A6L0Y5)
molecular function
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0047475    phenylacetate-CoA ligase activity    Catalysis of the reaction: ATP + CoA + phenylacetate = AMP + diphosphate + H(+) + phenylacetyl-CoA.
biological process
    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.
    GO:0010124    phenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylacetate.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3lax)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lax)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3lax
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A6L0Y5_BACV8 | A6L0Y5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  A6L0Y5_BACV8 | A6L0Y5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3LAX)

(-) Related Entries Specified in the PDB File

3gxs THIS DEPOSIT IS TO REPLACE 3GXS. RELATED ID: APC62324.1 RELATED DB: TARGETDB