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 BGLB WITH NATURAL SUBSTRATE
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  14 Nov 12  (Deposition) - 19 Dec 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.14
Chains :  Asym./Biol. Unit :  A
Keywords :  Glucosidase, Beta-Glucosidase, Bglb, Bgl, Hydrolase, Glycosidase, Tim Barrel, Carbohydrate/Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Nam, M. W. Sung, K. Y. Hwang
Structural Insights Into The Substrate Recognition Properties Of Beta-Glucosidase.
Biochem. Biophys. Res. Commun. V. 391 1131 2010
PubMed-ID: 20005197  |  Reference-DOI: 10.1016/J.BBRC.2009.12.038

(-) Compounds

Molecule 1 - BETA-GLUCOSIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 39-482
    Gene: BGLA
    Mutation: YES
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133

 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
1BGC1Ligand/IonBETA-D-GLUCOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:57 , HIS A:158 , ASN A:202 , GLU A:203 , TYR A:332 , TRP A:360 , GLU A:387 , TRP A:434 , GLU A:441 , TRP A:442 , PHE A:450BINDING SITE FOR RESIDUE BGC A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HZ8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:218 -Pro A:219
2Pro A:343 -Pro A:344
3Ser A:353 -Pro A:354
4Trp A:434 -Ser A:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 4HZ8)

(-) 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:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4hz8a_ A: Beta-glucosidase A                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.hhhhhh..........hhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhh..hhhhhhh....eeeee....eeeee......eeee.............hhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hz8 A  42 KFPEGFLWGAATSSYQIEGAWNEDGKGESIWDRFTRIPGKIKNGDSGDVACDHYHRYEQDLDLMRQLGLKTYRFSIAWARIQPDSSRQINQRGLDFYRRLVEGLHKRDILPMATLYHWDLPQWVEDEGGWLSRESASRFAEYTHALVAALGDQIPLWVTHNEPMVTVWAGYHMGLFAPGLKDPTLGGRVAHHLLLSHGQALQAFRALSPAGSQMGITLNFNTIYPVSAEPADVEAARRMHSFQNELFLEPLIRGQYNQATLMAYPNLPEFIAPEDMQTISAPIDFLGVNYYNPMRVKSSPQPPGIEVVQVESPVTAMGWEIAPEGLYDLLMGITRTYGKLPIYITENGAAFDDQPDQSGQVNDPQRVGYFQGHIGAARRALADGVDLRGYYAWSLLDNFEWAEGYSKRFGIIYVDFETQQRTLKQSAQWYRDVIANNGL 480
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471
   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 ; only for superseded entry 3FJ0: 1,1)

(no "CATH Domain" information available for 4HZ8, only for superseded entry 3FJ0 replaced by 4HZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HZ8)

(-) Gene Ontology  (8, 8)

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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:218 - Pro A:219   [ RasMol ]  
    Pro A:343 - Pro A:344   [ RasMol ]  
    Ser A:353 - Pro A:354   [ RasMol ]  
    Trp A:434 - Ser A:435   [ 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 | Asym./Biol. Unit - sites 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
  4hz8
    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
  Q0GMU3_9BACT | Q0GMU3
    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
  Q0GMU3_9BACT | Q0GMU3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q0GMU3_9BACT | Q0GMU3: 3cmj 4hz6 4hz7

(-) Related Entries Specified in the PDB File

4hz6 4hz7