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 :  CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY ETHYL ALCOHOL
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  11 Apr 09  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hsl, Este5, Esterase, Lipase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Y. Hwang, K. H. Nam
Crystal Structure Of Este5, Was Soaked By Organic Solvent
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ESTERASE/LIPASE
    Chains: A
    EC Number: 3.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ESTE5
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133
    Other Details: SOIL METAGENOME LIBRARY
    Synonym: ESTE5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3H1A)

(-) Sites  (0, 0)

(no "Site" information available for 3H1A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H1A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:109 -Pro A:110
2Phe A:114 -Pro A:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H1A)

(-) Exons   (0, 0)

(no "Exon" information available for 3H1A)

(-) 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:296
 aligned with Q0GMU2_9BACT | Q0GMU2 from UniProtKB/TrEMBL  Length:297

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
         Q0GMU2_9BACT     2 AGPEIVKLKKILREKAVPPGTEVPLDVMRKGMEKVAFKAADDIQVEQVTVAGCAAEWVRAPGCQAGKAILYLHGGGYVMGSINTHRSMVGEISRASQAAALLLDYRLAPEHPFPAAVEDGVAAYRWLLDQGFKPQHLSISGDSAGGGLVLAVLVSARDQGLPMPASAIPISPWADMTCTNDSFKTRAEADPMVAPGGINKMAARYLNGADAKHPYASPNFANLKGLPPLLIHVGRDEVLLDDSIKLDAKAKADGVKSTLEIWDDMIHVWHAFHPMLPEGKQAIVRVGEFMREQWAA 297
               SCOP domains d3h1aa_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhh........eeeeeee..eeeeeee........eeeee........hhhhhhhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhh..hhh.eeeeeehhhhhhhhhhhhhhhhh......eeeee..........hhhhhh.........hhhhhhhhhhhh.........hhhhh.......eeeeee....hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h1a A   2 AGPEIVKLKKILREKAVPPGTEVPLDVMRKGMEKVAFKAADDIQVEQVTVAGCAAEWVRAPGCQAGKAILYLHGGGYVMGSINTHRSMVGEISRASQAAALLLDYRLAPEHPFPAAVEDGVAAYRWLLDQGFKPQHLSISGDSAGGGLVLAVLVSARDQGLPMPASAIPISPWADMTCTNDSFKTRAEADPMVAPGGINKMAARYLNGADAKHPYASPNFANLKGLPPLLIHVGRDEVLLDDSIKLDAKAKADGVKSTLEIWDDMIHVWHAFHPMLPEGKQAIVRVGEFMREQWAA 297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H1A)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0GMU2_9BACT | Q0GMU2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
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.

 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 3h1a)
 
  Sites
(no "Sites" information available for 3h1a)
 
  Cis Peptide Bonds
    Ala A:109 - Pro A:110   [ RasMol ]  
    Phe A:114 - Pro A:115   [ 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
  3h1a
    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
  Q0GMU2_9BACT | Q0GMU2
    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.-
    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
  Q0GMU2_9BACT | Q0GMU2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q0GMU2_9BACT | Q0GMU2: 3fak 3g9t 3g9u 3g9z 3h17 3h18 3h19 3h1b 3l1h 3l1i 3l1j 3v9a

(-) Related Entries Specified in the PDB File

3fak CRYSTAL STRUCTURE OF ESTE5 (NATIVE)
3g9u CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY P-NITROPHENYL BUTYRATE FOR 5MIN
3g9v CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY P-NITROPHENYL BUTYRATE FOR 5SEC
3g9z CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY P-NITROPHENYL CAPRYLATE
3h17 CRYSTAL STRUCTURE OF ESTE5-PMSF (I)
3h18 CRYSTAL STRUCTURE OF ESTE5-PMSF (II)
3h19 CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY METHYL ALCOHOL
3h1b CRYSTAL STRUCTURE OF ESTE5, WAS SOAKED BY ISOPROPYL ALCOHOL