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 :  2.3A CRYSTAL STRUCTURE OF PHOSPHO-BETA-GLUCOSIDASE
 
Authors :  V. Tereshko, I. Dementieva, Y. Kim, F. Collat, A. Joachimiak, A. Kossia Midwest Center For Structural Genomics (Mcsg)
Date :  28 Jan 04  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tereshko, I. Dementieva, Y. Kim, F. Collat, A. Joachimiak, A. Kossiakoff
2. 3A Crystal Structure Of Phospho-Beta-Glucosidase, Lich Gene Product From Bacillus Stearothermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 6-PHOSPHO-BETA-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.86
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LICH
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1S6Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S6Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S6Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1S6Y)

(-) 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:416
 aligned with P84135_GEOSE | P84135 from UniProtKB/TrEMBL  Length:450

    Alignment length:439
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436         
         P84135_GEOSE     7 RLKIATIGGGSSYTPELVEGLIKRYHELPVGELWLVDIPEGKEKLEIVGALAKRXVEKAGVPIEIHLTLDRRRALDGADFVTTQFRVGGLEARAKDERIPLKYGVIGQETNGPGGLFKGLRTIPVILDIIRDXEELCPDAWLINFTNPAGXVTEAVLRYTKQEKVVGLCNVPIGXRXGVAKLLGVDADRVHIDFAGLNHXVFGLHVYLDGVEVTEKVIDLVAHPDRSGVTXKNIVDLGWEPDFLKGLKVLPCPYHRYYFQTDKXLAEELEAAKTKGTRAEVVQQLEKELFELYKDPNLAIKPPQLEKRGGAYYSDAACSLISSIYNDKRDIQPVNTRNNGAIASISAESAVEVNCVITKDGPKPIAVGDLPVAVRGLVQQIKSFERVAAEAAVTGDYQTALVAXTINPLVPSDTIAKQILDEXLEAHKEYLPQFFKQAK 445
               SCOP domains d1s6ya1 A:4-172 6-phospho-beta-glucosidase                                                                                                                               d1s6ya2 A:173-445 6-phospho-beta-glucosidase                                                                                                                                                                                                                                   SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------1s6yA02 A:171-445 L-2-Hydroxyisocaproate Dehydrogenase, s            ubunit A, domain 2                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhh...eeee....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh.hhh.eeeeeeee..eeeeeeeee..eehhhhhhhhhh..------------...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....-----------....hhhhhhhhhhhhhhhh...eeeeeee............eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6y A   4 RLKIATIGGGSSYTPELVEGLIKRYHELPVGELWLVDIPEGKEKLEIVGALAKRmVEKAGVPIEIHLTLDRRRALDGADFVTTQFRVGGLEARAKDERIPLKYGVIGQETNGPGGLFKGLRTIPVILDIIRDmEELCPDAWLINFTNPAGmVTEAVLRYTKQEKVVGLCNVPIGmRmGVAKLLGVDADRVHIDFAGLNHmVFGLHVYLDGVEVTEKVIDLVAHP------------LGWEPDFLKGLKVLPCPYHRYYFQTDKmLAEELEAAKTKGTRAEVVQQLEKELFELYKDP-----------RGGAYYSDAACSLISSIYNDKRDIQPVNTRNNGAIASISAESAVEVNCVITKDGPKPIAVGDLPVAVRGLVQQIKSFERVAAEAAVTGDYQTALVAmTINPLVPSDTIAKQILDEmLEAHKEYLPQFFKQAK 445
                                    13        23        33        43        53    |   63        73        83        93       103       113       123       133  |    143       153|      163       173    | |183       193       203       213       223   |     -      |243       253       263   |   273       283       293     |   -       316       326       336       346       356       366       376       386       396       406   |   416       426  |    436         
                                                                                 58-MSE                                                                       136-MSE           154-MSE                 178-MSE                  203-MSE                 227          240                        267-MSE                         299         314                                                                                             410-MSE            429-MSE            
                                                                                                                                                                                                          180-MSE
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S6Y)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P84135_GEOSE | P84135)
molecular function
    GO:0008706    6-phospho-beta-glucosidase activity    Catalysis of the reaction: 6-phospho-beta-D-glucoside-(1,4)-D-glucose + H2O = D-glucose 6-phosphate + glucose.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1s6y)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s6y)
 

(-) 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
  1s6y
    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
  P84135_GEOSE | P84135
    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
  P84135_GEOSE | P84135
    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 1S6Y)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1S6Y)