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 :  CRYSTAL STRUCTURE ANALYSIS OF A TYPE II COHESIN DOMAIN FROM THE CELLULOSOME OF ACETIVIBRIO CELLULOLYTICUS
 
Authors :  F. Frolow, I. Noach, S. Rosenheck, R. Lamed, X. Qi, L. J. W. Shimon, E. A. Bayer
Date :  17 Sep 03  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Keywords: Cohesins Type Ii; Cellulosome; , Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Noach, F. Frolow, H. Jakoby, S. Rosenheck, L. W. Shimon, R. Lamed, E. A. Bayer
Crystal Structure Of A Type-Ii Cohesin Module From The Bacteroides Cellulosolvens Cellulosome Reveals Novel And Distinctive Secondary Structural Elements.
J. Mol. Biol. V. 348 1 2005
PubMed-ID: 15808849  |  Reference-DOI: 10.1016/J.JMB.2005.02.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELLULOSOMAL SCAFFOLDIN ADAPTOR PROTEIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: COHESIN II DOMAIN FROM CELLULOSOME ASSEMBLY
    Gene: SCAB
    Organism Scientific: ACETIVIBRIO CELLULOLYTICUS
    Organism Taxid: 35830

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1QZN)

(-) Sites  (0, 0)

(no "Site" information available for 1QZN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QZN)

(-) 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:171
 aligned with Q7WYN3_9FIRM | Q7WYN3 from UniProtKB/TrEMBL  Length:942

    Alignment length:171
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198 
         Q7WYN3_9FIRM    29 PTSSIEIVLDKTTASVGEIVTASINIKNITNFSGCQLNMKYDPAVLQPVTSSGVAYTKSTMPGAGTILNSDFNLRQVADNDLEKGILNFSKAYVSLDDYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPNAIDGTVLFDWNGDRIQSGYSVIQPAVINLDMIKAS 199
               SCOP domains d1qzna_ A: Cellulosomal scaffoldin adaptor protein B, ScaB                                                                                                                  SCOP domains
               CATH domains 1qznA00 A:3-173  [code=2.60.40.680, no name defined]                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeeee....eeeeeeeee.....eeee.............ee.........eeeee.......eeeeeeee.hhhhhhhhh.....eeeeeeeeee.....eeeee............eeeee..........eee..eeehhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qzn A   3 PTSSIEIVLDKTTASVGEIVTASINIKNITNFSGCQLNMKYDPAVLQPVTSSGVAYTKSTMPGAGTILNSDFNLRQVADNDLEKGILNFSKAYVSLDDYRTAAAPEQTGTVAVVKFKVLKEETSSISFEDTTSVPNAIDGTVLFDWNGDRIQSGYSVIQPAVINLDMIKAS 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7WYN3_9FIRM | Q7WYN3)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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
(no "Ligands, Modified Residues, Ions" information available for 1qzn)
 
  Sites
(no "Sites" information available for 1qzn)
 
  Cis Peptide Bonds
    Gln A:161 - Pro A:162   [ 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 ](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
  1qzn
    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
  Q7WYN3_9FIRM | Q7WYN3
    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
  Q7WYN3_9FIRM | Q7WYN3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7WYN3_9FIRM | Q7WYN3: 1zv9 3bwz 3f2l 3fnk 3ghp 3l8q 4u3s 4uyp 4uyq 4wi0

(-) Related Entries Specified in the PDB File

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