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 :  THE SEMET STRUCTURE OF THE FAMILY 46 CARBOHYDRATE-BINDING MODULE (CBM46) OF ENDO-BETA-1,4-GLUCANASE B (CEL5B) FROM BACILLUS HALODURANS
 
Authors :  I. Venditto, H. Santos, L. M. A. Ferreira, K. Sakka, C. M. G. A. Fontes, S.
Date :  04 Sep 14  (Deposition) - 25 Feb 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Binding Protein, Carbohydrate Binding Protein, Carbohydrate-Binding Module Family 46, Cbm46, Cel5B, Bacillus Halodurans, Semet Derivative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Venditto, S. Najmudin, A. S. Luis, L. M. Ferreira, K. Sakka, J. P. Knox, H. J. Gilbert, C. M. Fontes
Family 46 Carbohydrate-Binding Modules Contribute To The Enzymatic Hydrolysis Of Xyloglucan And Beta-1, 3-1, 4-Glucans Through Distinct Mechanisms.
J. Biol. Chem. V. 290 10572 2015
PubMed-ID: 25713075  |  Reference-DOI: 10.1074/JBC.M115.637827
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-BETA-1,4-GLUCANASE (CELULASE B)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    Fragment: CARBOHYDRATE BINDING MODULE FAMILY 46, UNP RESIDUES 457-563
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665
    Other Details: SELENOMETHIONYLATED DERIVATIVE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:554 , GLY B:555 , ASN B:556 , GLN B:557BINDING SITE FOR RESIDUE SO4 B1564

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UZ8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:478 -Asn A:479
2Asn A:479 -Gly A:480
3Gly A:544 -Glu A:545
4Gly B:544 -Glu B:545

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 4UZ8)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...eeee.......eeeeeeee....................eeeehhh.eeeehhhhhhh...eeeeeeeee....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4uz8 A 457 YRTPVLQSTQGHVSNFSIPASFNGNSLATmEAVYVDGGNAGPQDWTSFKEFGYAFSPSYDANEmKLTEAFFREVRDGEVRLTFHFWSGETVNYTIIKNGNQVTGIAA 563
                                   466       476       486       496       506       516   |   526       536       546       556       
                                                       486-MSE                           520-MSE                                       


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eeee.......eeeeeeee....................eeeehhh.eeeehhhhhhh...eeeeeeeee....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4uz8 B 458 RTPVLQSTQGHVSNFSIPASFNGNSLATmEAVYVDGGNAGPQDWTSFKEFGYAFSPSYDANEmKLTEAFFREVRDGEVRLTFHFWSGETVNYTIIKNGNQVTGIAA 563
                                   467       477       487       497       507       517  |    527       537       547       557      
                                                      486-MSE                           520-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  (0, 0)

(no "SCOP Domain" information available for 4UZ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UZ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UZ8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:479 - Gly A:480   [ RasMol ]  
    Gly A:544 - Glu A:545   [ RasMol ]  
    Gly B:544 - Glu B:545   [ RasMol ]  
    Phe A:478 - Asn A:479   [ 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
  4uz8
    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
  Q9KF82_BACHD | Q9KF82
    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
  Q9KF82_BACHD | Q9KF82
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9KF82_BACHD | Q9KF82: 4uzn 4v2x

(-) Related Entries Specified in the PDB File

4uyp HIGH RESOLUTION STRUCTURE OF THE THIRD COHESIN SCAC IN COMPLEX WITH THE SCAB DOCKERIN WITH A MUTATION IN THE N-TERMINAL HELIX (IN TO SI) FROM ACETIVIBRIO CELLULOLYTICUS DISPLAYING A TYPE I INTERACTION.
4uyq HIGH RESOLUTION STRUCTURE OF THE THIRD COHESIN SCAC IN COMPLEX WITH THE SCAB DOCKERIN WITH A MUTATION IN THE C-TERMINAL HELIX (IN TO SI) FROM ACETIVIBRIO CELLULOLYTICUS DISPLAYING A TYPE I INTERACTION.
4uzn THE NATIVE STRUCTURE OF THE FAMILY 46 CARBOHYDRATE- BINDING MODULE (CBM46) OF ENDO-BETA-1,4-GLUCANASE B (CEL5B) FROM BACILLUS HALODURANS
4uzp HIGH RESOLUTION STRUCTURE OF THE FULL LENGTH TRI- MODULAR ENDO-BETA-1,4-GLUCANASE B (CEL5B) FROM BACILLUS HALODURANS