Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CBM31 FROM BETA-1,3-XYLANASE
 
Authors :  H. Hashimoto, Y. Tamai, F. Okazaki, Y. Tamaru, T. Shimizu, T. Araki, M. S
Date :  18 May 05  (Deposition) - 13 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  D,E,F,G,H,I
Keywords :  Carbohydrate-Binding Module, Family 31 Cbm, Beta-1, 3-Xylanase, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, Y. Tamai, F. Okazaki, Y. Tamaru, T. Shimizu, T. Araki, M. Sato
The First Crystal Structure Of A Family 31 Carbohydrate-Binding Module With Affinity To Beta-1, 3-Xylan
Febs Lett. V. 579 4324 2005
PubMed-ID: 16061225  |  Reference-DOI: 10.1016/J.FEBSLET.2005.06.062

(-) Compounds

Molecule 1 - BETA-1,3-XYLANASE
    Chains: D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 378-469
    Organism Scientific: ALCALIGENES SP.
    Organism Taxid: 118970
    Strain: XY-234

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : DEFGHI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2COV)

(-) Sites  (0, 0)

(no "Site" information available for 2COV)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1D:382 -D:468
2D:413 -D:418
3E:382 -E:468
4E:413 -E:418
5F:382 -F:468
6F:413 -F:418
7G:382 -G:468
8G:413 -G:418
9H:382 -H:468
10H:413 -H:418
11I:382 -I:468
12I:413 -I:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2COV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2COV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2COV)

(-) Exons   (0, 0)

(no "Exon" information available for 2COV)

(-) 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 D from PDB  Type:PROTEIN  Length:92
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:92
                                   387       397       407       417       427       437       447       457       467  
           3XYN_ALCSP   378 PPENCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2cov D 378 PPENCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
                                   387       397       407       417       427       437       447       457       467  


Chain E from PDB  Type:PROTEIN  Length:92
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:92
                                   387       397       407       417       427       437       447       457       467  
           3XYN_ALCSP   378 PPENCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2cov E 378 PPENCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
                                   387       397       407       417       427       437       447       457       467  


Chain F from PDB  Type:PROTEIN  Length:87
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:87
                                   391       401       411       421       431       441       451       461       
           3XYN_ALCSP   382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2cov F 382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
                                   391       401       411       421       431       441       451       461       


Chain G from PDB  Type:PROTEIN  Length:88
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:88
                                   390       400       410       420       430       440       450       460        
           3XYN_ALCSP   381 NCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeeehhh.eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 2cov G 381 NCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
                                   390       400       410       420       430       440       450       460        


Chain H from PDB  Type:PROTEIN  Length:87
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:87
                                   391       401       411       421       431       441       451       461       
           3XYN_ALCSP   382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeeehhh.eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2cov H 382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVC 468
                                   391       401       411       421       431       441       451       461       


Chain I from PDB  Type:PROTEIN  Length:88
 aligned with 3XYN_ALCSP | Q8RS40 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:88
                                   391       401       411       421       431       441       451       461        
           3XYN_ALCSP   382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..eeeeeee........eeeee..eeee.eee..eeeeeee.....eeeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 2cov I 382 CQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLGQDYKLTFKVEDRYGQGQQILDRNITFTTQVCN 469
                                   391       401       411       421       431       441       451       461
   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 2COV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2COV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2COV)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D,E,F,G,H,I   (3XYN_ALCSP | Q8RS40)
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.
    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:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0033914    xylan 1,3-beta-xylosidase activity    Catalysis of the hydrolysis of successive xylose residues from the non-reducing termini of (1->3)-beta-D-xylans.
    GO:0033905    xylan endo-1,3-beta-xylosidase activity    Catalysis of the random hydrolysis of (1->3)-beta-D-glycosidic linkages in (1->3)-beta-D-xylans.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

 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 2cov)
 
  Sites
(no "Sites" information available for 2cov)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cov)
 

(-) 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
  2cov
    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
  3XYN_ALCSP | Q8RS40
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  3XYN_ALCSP | Q8RS40
    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 2COV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2COV)