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 :  C-TERMINAL ESTERASE DOMAIN OF LC-EST1
 
Authors :  H. Okano, X. Hong, C. Angkawidjaja, S. Kanaya
Date :  26 Aug 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Leaf-Branch Compost; Metagenome, Alpha/Beta Hydrolase Fold, Esterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Okano, X. Hong, E. Kanaya, C. Angkawidjaja, S. Kanaya
Structural And Biochemical Characterization Of A Metagenome-Derived Esterase With A Long N-Terminal Extensio
Protein Sci. 2014
PubMed-ID: 25348365  |  Reference-DOI: 10.1002/PRO.2591

(-) Compounds

Molecule 1 - LC-EST1C
    Chains: A, B
    EC Number: 3.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNCULTURED ORGANISM
    Organism Taxid: 155900

 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 3WYD)

(-) Sites  (0, 0)

(no "Site" information available for 3WYD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WYD)

(-) 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:193
 aligned with A0A0A6YVN5_9 | A0A0A6YVN5 from UniProtKB/TrEMBL  Length:208

    Alignment length:199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
         A0A0A6YVN5_9     2 PYRLYVPTTYDGTKAFPLVIALHGMGGDENSYFDSYQRGAFMIEAENRGYIVACPKGRQPASMYVGPAERDVMDVIAEVRRDYKIDPDRIYMTGHSMGGYGTWSIAMNHPDVFAALAPVAGGGNPLGMANIAHIPQLVVHGDNDKTVPVERSRVMVEAAKKHGTEIKYIEIPGGDHVSVAARTFKDVFDWFDSHKRKRP 200
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..........eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee..------..hhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyd A 304 PYRLYVPTTYDGTKAFPLVIALHGMGGDENSYFDSYQRGAFMIEAENRGYIVACPKG------YVGPAERDVMDVIAEVRRDYKIDPDRIYMTGHSMGGYGTWSIAMNHPDVFAALAPVAGGGNPLGMANIAHIPQLVVHGDNDKTVPVERSRVMVEAAKKHGTEIKYIEIPGGDHVSVAARTFKDVFDWFDSHKRKRP 502
                                   313       323       333       343       353      |  -   |   373       383       393       403       413       423       433       443       453       463       473       483       493         
                                                                                  360    367                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with A0A0A6YVN5_9 | A0A0A6YVN5 from UniProtKB/TrEMBL  Length:208

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
         A0A0A6YVN5_9     2 PYRLYVPTTYDGTKAFPLVIALHGMGGDENSYFDSYQRGAFMIEAENRGYIVACPKGRQPASMYVGPAERDVMDVIAEVRRDYKIDPDRIYMTGHSMGGYGTWSIAMNHPDVFAALAPVAGGGNPLGMANIAHIPQLVVHGDNDKTVPVERSRVMVEAAKKHGTEIKYIEIPGGDHVSVAARTFKDVFDWFDSHKRK 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..........eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee..------..hhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyd B 304 PYRLYVPTTYDGTKAFPLVIALHGMGGDENSYFDSYQRGAFMIEAENRGYIVACPKG------YVGPAERDVMDVIAEVRRDYKIDPDRIYMTGHSMGGYGTWSIAMNHPDVFAALAPVAGGGNPLGMANIAHIPQLVVHGDNDKTVPVERSRVMVEAAKKHGTEIKYIEIPGGDHVSVAARTFKDVFDWFDSHKRK 500
                                   313       323       333       343       353      |  -   |   373       383       393       403       413       423       433       443       453       463       473       483       493       
                                                                                  360    367
   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 3WYD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WYD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WYD)

 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 3wyd)
 
  Sites
(no "Sites" information available for 3wyd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3wyd)
 

(-) 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
  3wyd
    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
  A0A0A6YVN5_9 | A0A0A6YVN5
    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)
  3.1.1.1
    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
  A0A0A6YVN5_9 | A0A0A6YVN5
    Protein Disorder Prediction: DisEMBL | 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 3WYD)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WYD)