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 :  CELLVIBRIO JAPONICUS MANNANASE CJMAN26C MANNOBIOSE-BOUND FORM
 
Authors :  A. Cartmell, E. Topakas, V. M. -A. Ducros, M. D. L. Suits, G. J. Davies, H. J. Gilbert
Date :  01 Jul 08  (Deposition) - 16 Sep 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cellvibrio Japonicus, Mannanase, Cjman26C, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Cartmell, E. Topakas, V. M. -A. Ducros, M. D. L. Suits, G. J. Davies, H. J. Gilbert
The Cellvibrio Japonicus Mannanase Cjman26C Displays A Unique Exo-Mode Of Action That Is Conferred By Subtle Changes To The Distal Region Of The Active Site.
J. Biol. Chem. V. 283 34403 2008
PubMed-ID: 18799462  |  Reference-DOI: 10.1074/JBC.M804053200

(-) Compounds

Molecule 1 - CELLVIBRIO JAPONICUS MANNANASE CJMAN26C
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 155077

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MAB1Ligand/IonMANNOBIOSE
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:130 , HIS A:156 , TRP A:167 , GLU A:221 , ASP A:295 , TYR A:297 , TRP A:373 , ARG A:374 , GLN A:385 , HOH A:2028 , HOH A:2314 , HOH A:2315 , HOH A:2316 , HOH A:2317 , HOH A:2318BINDING SITE FOR RESIDUE MAB A 1420
2AC2SOFTWARETYR A:403 , GLN A:404 , SER A:405 , HOH A:2301 , HOH A:2309BINDING SITE FOR RESIDUE NA A 1421

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VX7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VX7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VX7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VX7)

(-) Exons   (0, 0)

(no "Exon" information available for 2VX7)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d2vx7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2vx7A00 A:53-419 Glycosidases                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh...eeeeee...............hhhhhhhh....eeeee..hhhhh........hhhhhhhhhhhhhhh..eeeee.................hhhhhh....hhhhhhhhhhhhhhhhhh..ee.....ee...eeee...................hhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh....hhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhh..hhhhh.eeee....hhhhhh............hhhhhhhhhhh..eehhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vx7 A  53 LPALIDTQATAETRALYRNLAKLRYKHLLFGHEDSLAYGVHWEGDMDRSDVRDVTGANPAVYGWELGGLELGHTANLDAVNFEKMQHWIKAGYSRGGVITISWHVFNPVSGGNSWDKTPAVHELIPGGARHATLKAYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTVHYLRDEKKLRNLIYAYSPDRSRIDMANFEAGYLYGYPGDAYVDIIGLDNYWDVGHEANTASADEQKAALTASLKQLVQIARSKGKIAALTATGNNRLTIDNFWTERLLGPISADADASEIAYVMVWRNANLAREKSEQFFAPFPGQATADDFKRFYQSEVVLFEDELPPLYR 419
                                    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       412
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VX7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2VX7)

 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
    MAB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vx7)
 

(-) 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
  2vx7
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.-
    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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2VX7)

(-) Related Entries Specified in the PDB File

2vx4 CELLVIBRIO JAPONICUS MANNANASE CJMAN26C NATIVE FORM
2vx5 CELLVIBRIO JAPONICUS MANNANASE CJMAN26C MANNOSE -BOUND FORM
2vx6 CELLVIBRIO JAPONICUS MANNANASE CJMAN26C GAL1MAN4 -BOUND FORM