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 CELLOBIOSE 2-EPIMERASE IN COMPLEX WITH CELLOBIITOL
 
Authors :  T. Fujiwara, W. Saburi, I. Tanaka, M. Yao
Date :  21 Oct 13  (Deposition) - 25 Dec 13  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  (Alpha/Alpha)6 Barrel Fold, Epimerase, Carbohydrate/Sugar Binding, Epimerization, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fujiwara, W. Saburi, H. Matsui, H. Mori, M. Yao
Structural Insights Into The Epimerization Of Beta-1, 4-Linked Oligosaccharides Catalyzed By Cellobiose 2-Epimerase, The Sole Enzyme Epimerizing Non-Anomeric Hydroxyl Groups Of Unmodified Sugars
J. Biol. Chem. V. 289 3405 2014
PubMed-ID: 24362032  |  Reference-DOI: 10.1074/JBC.M113.531251

(-) Compounds

Molecule 1 - CELLOBIOSE 2-EPIMERASE
    Chains: A
    EC Number: 5.1.3.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CE
    Organism Scientific: RHODOTHERMUS MARINUS
    Organism Taxid: 29549
    Strain: JCM9785
    Synonym: CE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CL1Ligand/IonCHLORIDE ION
3GLO1Ligand/IonD-GLUCOSE IN LINEAR FORM
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:66 , GLY A:387 , TYR A:389 , HIS A:390BINDING SITE FOR RESIDUE CL A 501
2AC2SOFTWAREGLY A:41 , GLY A:42 , ARG A:89 , ARG A:92 , TYR A:93 , ARG A:96 , ARG A:352 , HOH A:659 , HOH A:717BINDING SITE FOR RESIDUE PO4 A 504
3AC3SOFTWAREARG A:66 , TYR A:124 , SER A:185 , ASP A:188 , ASN A:196 , HIS A:200 , HIS A:259 , GLU A:262 , TRP A:321 , TRP A:322 , TRP A:385 , HIS A:390 , HOH A:632 , HOH A:636 , HOH A:689 , HOH A:720 , HOH A:819 , HOH A:827BINDING SITE FOR DI-SACCHARIDE BGC A 502 AND GLO A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WKI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WKI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WKI)

(-) Exons   (0, 0)

(no "Exon" information available for 3WKI)

(-) 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:407
 aligned with CEEP_RHOMR | F8WRK9 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:407
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       
           CEEP_RHOMR     3 TETIPDVRRLRALQAEVHEELTENILKFWATRTHDPVHGGFVGRVGPDGRPHPEAPRGAILNARILWTFAAAYRQLGTPLYREMAERAYRYFVRHFVDAEHGGVYWMVAADGRPLDTRKHVYAQSFAIYALSEWHRATGGEAALALARSIYDLIETHCADRVHGGYVEACDRAWRPLEDARLSAKDAPEPRSMNTHLHVLEAYANLYRVWPETELAARLQALIELFLRAIYHPATGHLILFFDERWRPRSRAVSFGHDIEASWLLLEAVDVLGQATLRPRVQQASLHLARATLAEGRAPDGSLYYEIGEQGHLDTDRHWWPQAEALVGFLNAYQESGEVLFYEAAEDVWRYIRERQRDTRGGEWFARVRDDGAPYPDDKVDFWKGPYHNGRACLEAIQRLRHLLEHV 409
               SCOP domains d3wkia_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee.....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee....................eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..........ee...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........ee.....ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee.................hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wki A   3 TETIPDVRRLRALQAEVHEELTENILKFWATRTHDPVHGGFVGRVGPDGRPHPEAPRGAILNARILWTFAAAYRQLGTPLYREMAERAYRYFVRHFVDAEHGGVYWMVAADGRPLDTRKHVYAQSFAIYALSEWHRATGGEAALALARSIYDLIETHCADRVHGGYVEACDRAWRPLEDARLSAKDAPEPRSMNTHLHVLEAYANLYRVWPETELAARLQALIELFLRAIYHPATGHLILFFDERWRPRSRAVSFGHDIEASWLLLEAVDVLGQATLRPRVQQASLHLARATLAEGRAPDGSLYYEIGEQGHLDTDRHWWPQAEALVGFLNAYQESGEVLFYEAAEDVWRYIRERQRDTRGGEWFARVRDDGAPYPDDKVDFWKGPYHNGRACLEAIQRLRHLLEHV 409
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
   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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WKI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WKI)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CEEP_RHOMR | F8WRK9)
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:0047736    cellobiose epimerase activity    Catalysis of the reaction: cellobiose = D-glucosyl-D-mannose.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

 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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3wki)
 

(-) 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
  3wki
    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
  CEEP_RHOMR | F8WRK9
    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)
  5.1.3.11
    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
  CEEP_RHOMR | F8WRK9
    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
        CEEP_RHOMR | F8WRK9: 3wkf 3wkg 3wkh

(-) Related Entries Specified in the PDB File

3wkf THE SAME PROTEIN COMPLEXED WITH CELLOBIITOL