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 :  STRUCTURE OF CBM26 FROM BACILLUS HALODURANS AMYLASE
 
Authors :  A. B. Boraston, M. Healey, J. Klassen, E. Ficko-Blean, A. Lammerts Van Bueren, V. Law
Date :  07 Oct 05  (Deposition) - 17 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate-Binding Module, Starch Binding, Carbohydrate Binding, Glycoside Hydrolase, Amylose, Amylopectin, Malto-Oligosaccharide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Boraston, M. Healey, J. Klassen, E. Ficko-Blean, A. Lammerts Van Bueren, V. Law
A Structural And Functional Analysis Of Alpha- Glucan Recognition By Family 25 And 26 Carbohydrate-Binding Modules Reveals A Conserved Mode Of Starch Recognition
J. Biol. Chem. V. 281 587 2006
PubMed-ID: 16230347  |  Reference-DOI: 10.1074/JBC.M509958200

(-) Compounds

Molecule 1 - ALPHA-AMYLASE G-6
    Atcc: BAA-125
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-BHCBM6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET 28A
    Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 771-863
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: C-125
    Synonym: FAMILY 26 CARBOHYDRATE-BINDING MODULE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:6 , ASP A:15 , ASP A:48 , ASP A:85 , HOH A:2015BINDING SITE FOR RESIDUE CD A1099
2AC2SOFTWAREASP A:89 , HIS A:93 , HOH A:2001 , HOH A:2004 , HOH A:2079BINDING SITE FOR RESIDUE CD A1100
3AC3SOFTWAREGLU A:43 , HIS A:52 , GLU A:55 , HOH A:2043BINDING SITE FOR RESIDUE CD A1101
4AC4SOFTWAREGLY A:1 , HIS A:44 , HOH A:2002 , HOH A:2003 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE CD A1102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C3G)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:28 -Pro A:29
2Trp A:72 -Pro A:73
3Asp A:85 -Gly A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C3G)

(-) Exons   (0, 0)

(no "Exon" information available for 2C3G)

(-) 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:98
 aligned with Q9KFR4_BACHD | Q9KFR4 from UniProtKB/TrEMBL  Length:958

    Alignment length:106
                                   767       777       787       797       807       817       827       837       847       857      
         Q9KFR4_BACHD   758 GTIEETYTYTKSTGLTIYFKKPDSWGTPHLYYYDTNPKVDEPTWSEAPEMEHYEGDWYTHTIEGVESVRLLFKDRGTNQWPGPGEPGFFRDQDGWFDGEWHVDRPG 863
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------....eeeeeee.......eeeeeeeee..............eeee..eeeeeee...eeeeeeee....ee.......eee...eee...ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2c3g A   1 G--------HMASGLTIYFKKPDSWGTPHLYYYDTNPKVDEPTWSEAPEMEHYEGDWYTHTIEGVESVRLLFKDRGTNQWPGPGEPGFFRDQDGWFDGEWHVDRPG  98
                            |        2        12        22        32        42        52        62        72        82        92      
                            |        2                                                                                                
                            1
   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 2C3G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C3G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C3G)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9KFR4_BACHD | Q9KFR4)
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:2001070    starch binding    Interacting selectively and non-covalently with starch.
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.

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:28 - Pro A:29   [ RasMol ]  
    Asp A:85 - Gly A:86   [ RasMol ]  
    Trp A:72 - Pro A:73   [ 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
  2c3g
    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
  Q9KFR4_BACHD | Q9KFR4
    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
  Q9KFR4_BACHD | Q9KFR4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9KFR4_BACHD | Q9KFR4: 2c3h 2c3v 2c3w 2c3x

(-) Related Entries Specified in the PDB File

2c3h STRUCTURE OF CBM26 FROM BACILLUS HALODURANS AMYLASE IN COMPLEX WITH MALTOSE
2c3v STRUCTURE OF IODINATED CBM25 FROM BACILLUS HALODURANS AMYLASE
2c3w STRUCTURE OF CBM25 FROM BACILLUS HALODURANS AMYLASE IN COMPLEX WITH MALTOTETRAOSE
2c3x STRUCTURE OF IODINATED CBM25 FROM BACILLUS HALODURANS AMYLASE IN COMPLEX WITH MALTOTETRAOSE