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 :  THE COMPLEX STRUCTURE OF 6-PHOSPHO-BETA-GLUCOSIDASE BGLA-2 WITH THIOCELLOBIOSE-6P FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  W. L. Yu, Y. L Jiang, P. Andreas, W. Cheng, X. H. Bai, Y. M. Ren, J. Thompso C. Z. Zhou, Y. X. Chen
Date :  10 Jan 13  (Deposition) - 24 Apr 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  B,E
Keywords :  Hydrolysase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. L. Yu, Y. L. Jiang, A. Pikis, W. Cheng, X. H. Bai, Y. M. Ren, J. Thompson C. Z. Zhou, Y. Chen
Structural Insights Into The Substrate Specificity Of A 6-Phospho-&[Beta]-Glucosidase Bgla-2 From Streptococcus Pneumoniae Tigr4
J. Biol. Chem. V. 288 14949 2013
PubMed-ID: 23580646  |  Reference-DOI: 10.1074/JBC.M113.454751

(-) Compounds

Molecule 1 - 6-PHOSPHO-BETA-GLUCOSIDASE
    Chains: B, E
    EC Number: 3.2.1.86
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET
    Gene: BGLA-2, SP_0578
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
11FT2Ligand/Ion4-S-(6-O-PHOSPHONO-ALPHA-L-IDOPYRANOSYL)-4-THIO-BETA-D-GLUCOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:18 , HIS B:125 , TYR B:126 , ASN B:170 , GLU B:171 , SER B:174 , GLU B:364 , TRP B:415 , SER B:422 , MET B:423 , SER B:424 , TYR B:432 , HOH B:672BINDING SITE FOR RESIDUE 1FT B 501
2AC2SOFTWARETYR E:303 , TRP E:338 , GLU E:364 , TRP E:415 , SER E:422 , MET E:423 , SER E:424 , LYS E:430 , TYR E:432 , HOH E:615BINDING SITE FOR RESIDUE 1FT E 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IPN)

(-) 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 B from PDB  Type:PROTEIN  Length:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ipnb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhh....hhhhh...hhhhh......................hhhhhhhhhhhhhhhhh..eeeee.hhhhhh........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhh...eeeeee...eee...........ee.....ee.hhhhhhhhhhhhhhhh..eeeeee........ee.....ee..hhhhhhhhhhhhhhhhhhhhh...eeeeeee...................eee...........eeehhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ipn B   2 TIFPDDFLWGGAVAANQVEGAYNEDGKGLSVQDVLPKGGLGEATENPTEDNLKLIGIDFYHKYKEDISLFSEMGFNVFRTSIAWSRIFPKGDEEEPNEAGLKYYDELFDELHAHGIEPLVTLSHYETPLYLARKYHGWVDRRMIHFYEKFARTVLERYKDKVKYWLTFNEVNSVLELPFTSGGIDIPKENLSKQELYQAIHHELVASSLVTKIAREINSEFKVGCMVLAMPAYPMTPNPKDVWATHEYENLNYLFSDVHVRGYYPNYAKRYFKENDINIEFAAEDAELLKNYTVDFLSFSYYMSVTQSALPGLVNPYLESSEWGWQIDPIGLRIILNRYYDRYQIPLFIVENGLGAKDQLIKDELNNLTVQDDYRIQYMKEHLLQVAEALQDGVEIMGYTSWGCIDCVSMSTAQLSKRYGLIYVDRNDDGSGTLNRYKKMSFTWYKEVIESNGESLF 470
                                    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       301       311||     333       343       353       363       373       383       393       403       413       423       433       443       453       463       
                                                                                                                                                                                                                                                                                                                                                312|                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                 325                                                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4ipne_ E: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhh...hhhhh...hhhhh......................hhhhhhhhhhhhhhhh...eeeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eee...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhh...eeeeee...eee..hhhhh..........ee.....ee.hhhhhhhhhhhhhhhh..eeeeee........ee.....ee..hhhhhhhhhhhhhhhhhhhhh...eeeeeee...................eee...........eeehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ipn E   2 TIFPDDFLWGGAVAANQVEGAYNEDGKGLSVQDVLPKGGLGEATENPTEDNLKLIGIDFYHKYKEDISLFSEMGFNVFRTSIAWSRIFPKGDEEEPNEAGLKYYDELFDELHAHGIEPLVTLSHYETPLYLARKYHGWVDRRMIHFYEKFARTVLERYKDKVKYWLTFNEVNSVLELPFTSGGIDIPKENLSKQELYQAIHHELVASSLVTKIAREINSEFKVGCMVLAMPAYPMTPNPKDVWATHEYENLNYLFSDVHVRGYYPNYAKRYFKENDINIEFAAEDAELLKNYTVDFLSFSYYMSVTQSALPTQYNSGGLVNPYLESSEWGWQIDPIGLRIILNRYYDRYQIPLFIVENGLGAKDQLIKDELNNLTVQDDYRIQYMKEHLLQVAEALQDGVEIMGYTSWGCIDCVSMSTAQLSKRYGLIYVDRNDDGSGTLNRYKKMSFTWYKEVIESNGESLF 470
                                    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       301       311      |327       337       347       357       367       377       387       397       407       417       427       437       447       457       467   
                                                                                                                                                                                                                                                                                                                                                      318|                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                       325
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4IPN)

 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
    1FT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ipn)
 

(-) 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
  4ipn
    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
  A0A0H2UP35_S | A0A0H2UP35
    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)
  3.2.1.86
    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
  A0A0H2UP35_S | A0A0H2UP35
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UP35_S | A0A0H2UP35: 4ipl

(-) Related Entries Specified in the PDB File

4ipl