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 CYCLO(L-LEUCYL-L-PHENYLALANYL) SYNTHASE
 
Authors :  M. Moutiez, E. Schmitt, J. Seguin, R. Thai, E. Favry, Y. Mechulam, M. Gon
Date :  07 Apr 14  (Deposition) - 08 Oct 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Cyclodipeptide Synthase, Aminoacyl-Trna, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Moutiez, E. Schmitt, J. Seguin, R. Thai, E. Favry, P. Belin, Y. Mechulam, M. Gondry
Unravelling The Mechanism Of Non-Ribosomal Peptide Synthesi By Cyclodipeptide Synthases.
Nat Commun V. 5 5141 2014
PubMed-ID: 25284085  |  Reference-DOI: 10.1038/NCOMMS6141

(-) Compounds

Molecule 1 - CYCLO(L-LEUCYL-L-PHENYLALANYL) SYNTHASE
    ChainsA
    EC Number2.3.2.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE60
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneALBC
    MutationYES
    Organism ScientificSTREPTOMYCES NOURSEI
    Organism Taxid1971
    SynonymCYCLODIPEPTIDE SYNTHASE, CDPS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1XVE1Ligand/IonPHENYLMETHYL N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , CYS A:37 , MET A:152 , ALA A:155 , ASN A:159 , TYR A:178 , GLU A:182 , TYR A:202BINDING SITE FOR RESIDUE XVE A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q24)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q24)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q24)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q24)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q24 A  10 DHGMREEILGDRSRLIRQRGEHALIGICAGNSYFSQKNTVMLLQWAGQRFERTDVVYVDTHIDEMLIADGRSAQEAERSVKRTLKDLRRRLRRSLESVGDHAERFRVRSLSELQETPEYRAVRERTDRAFEEDAEFATACEDMVRAVVMNRPGDGVGISAEHLRAGLNYVLAEAPLFADSPGVFSVPSSVLCYHIDTPITAFLSRRETGFRAAEGQAYVVVRPQ 233
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    

   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 4Q24)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q24)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q24)

(-) Gene Ontology  (3, 3)

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
    XVE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4q24)
 

(-) 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
  4q24
    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
  CLPS_STRNR | Q8GED7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.2.20
    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
  CLPS_STRNR | Q8GED7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CLPS_STRNR | Q8GED73oqv

(-) Related Entries Specified in the PDB File

3oqv