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 FAMILY 30 CARBOHYDRATE BINDING MODULE
 
Authors :  Y. Horiguchi, M. Kono, A. Suzuki, T. Yamane, M. Arai, K. Sakka, K. Omiya
Date :  21 Jul 04  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cbm30, Carbohydrate Binding Module Family30, Celj, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Horiguchi, M. Kono, A. Suzuki, T. Yamane, M. Arai, K. Sakka, K. Omiya
Crystal Structure Of Family 30 Carbohydrate Binding Module
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCBM
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-205
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405
    Synonym: FAMILY 30 CARBOHYDRATE BINDING MODULE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:10 , GLN B:12 , ARG B:71 , HOH B:410BINDING SITE FOR RESIDUE SO4 B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WMX)

(-) 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:173
 aligned with A3DD30_CLOTH | A3DD30 from UniProtKB/TrEMBL  Length:1601

    Alignment length:173
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
         A3DD30_CLOTH    38 LLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSE 210
               SCOP domains d1wmxa_ A: Endoglucanase CelJ                                                                                                                                                 SCOP domains
               CATH domains 1wmxA00 A:8-180  [code=2.60.120.360, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeeee.............eeeeeee..eeeeeeee........eeeeee........hhhhh...eeeeeeee.......eeeeee...........eeeee.hhh.......eeeeee.hhh...........eeeeeee......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmx A   8 LLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSE 180
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177   


Chain A from PDB  Type:PROTEIN  Length:173
 aligned with P71140_CLOTM | P71140 from UniProtKB/TrEMBL  Length:1601

    Alignment length:173
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
         P71140_CLOTM    38 LLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSE 210
               SCOP domains d1wmxa_ A: Endoglucanase CelJ                                                                                                                                                 SCOP domains
               CATH domains 1wmxA00 A:8-180  [code=2.60.120.360, no name defined]                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeeee.............eeeeeee..eeeeeeee........eeeeee........hhhhh...eeeeeeee.......eeeeee...........eeeee.hhh.......eeeeee.hhh...........eeeeeee......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmx A   8 LLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSE 180
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177   


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with A3DD30_CLOTH | A3DD30 from UniProtKB/TrEMBL  Length:1601

    Alignment length:195
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         A3DD30_CLOTH    34 GYRKLLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSEDNEKSAPAIKVNQLGFIP 228
               SCOP domains d1wmxb_ B: Endoglucanase CelJ                                                                                                                                                                       SCOP domains
               CATH domains 1wmxB00 B:4-198  [code=2.60.120.360, no name defined]                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CelD_N-1wmxB01       Pfam domains
         Sec.struct. author .......eeee......eeeee.............eeeeeee..eeeeeeee........eeeeee........hhhhh...eeeeeeee.......eeeeee...........eeeee.hhh.......eeeeeehhhhh......hhh.eeeeeee......eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmx B   4 GYRKLLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSEDNEKSAPAIKVNQLGFIP 198
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with P71140_CLOTM | P71140 from UniProtKB/TrEMBL  Length:1601

    Alignment length:195
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         P71140_CLOTM    34 GYRKLLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSEDNEKSAPAIKVNQLGFIP 228
               SCOP domains d1wmxb_ B: Endoglucanase CelJ                                                                                                                                                                       SCOP domains
               CATH domains 1wmxB00 B:4-198  [code=2.60.120.360, no name defined]                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CelD_N-1wmxB01       Pfam domains
         Sec.struct. author .......eeee......eeeee.............eeeeeee..eeeeeeee........eeeeee........hhhhh...eeeeeeee.......eeeeee...........eeeee.hhh.......eeeeeehhhhh......hhh.eeeeeee......eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmx B   4 GYRKLLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLRGWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQHVKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSEDNEKSAPAIKVNQLGFIP 198
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CelD_N] (3)

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P71140_CLOTM | P71140)
molecular function
    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:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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.

Chain A,B   (A3DD30_CLOTH | A3DD30)
molecular function
    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:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wmx)
 

(-) 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
  1wmx
    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
  A3DD30_CLOTH | A3DD30
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  P71140_CLOTM | P71140
    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
  A3DD30_CLOTH | A3DD30
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  P71140_CLOTM | P71140
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        P71140_CLOTM | P71140: 2c26 2e0p 2eex 2ej1 2eqd
UniProtKB/TrEMBL
        A3DD30_CLOTH | A3DD30: 1wzx 2c26 2e0p 2eex 2ej1 2eqd
        P71140_CLOTM | P71140: 2c24 2c4x 2e4t 2eo7

(-) Related Entries Specified in the PDB File

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