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 STRUCTURE OF GH26 BETA-MANNANASE CJMAN26C FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH MANIFG
 
Authors :  R. J. Williams, J. Iglesias-Fernandez, J. Stepper, A. Jackson, A. J. Th E. C. Lowe, J. M. White, H. J. Gilbert, C. Rovira, G. J. Davies, S. J. Will
Date :  30 Oct 13  (Deposition) - 02 Apr 14  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Beta-Mannosidase, Mannosidase, Glycoside Hydrolase, Gh26, Gh113, Cazy, Enzyme-Carbohydrate Interaction, Mannose, Glycosidase Inhibition, Quantum Mechanics, Biocatalysis, Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Williams, J. Iglesias-Fernandez, J. Stepper, A. Jackson, A. J. Thompson, E. C. Lowe, J. M. White, H. J. Gilbert, C. Rovira, G. J. Davies, S. J. Williams
Combined Inhibitor Free-Energy Landscape And Structural Analysis Reports On The Mannosidase Conformational Coordinate.
Angew. Chem. Int. Ed. Engl. V. 53 1087 2014
PubMed-ID: 24339341  |  Reference-DOI: 10.1002/ANIE.201308334

(-) Compounds

Molecule 1 - ENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C
    Chains: A
    EC Number: 3.2.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 498211
    Strain: UEDA107
    Synonym: CJMAN26C BETA-MANNANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2IFM1Ligand/Ion5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
3NA2Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:403 , GLN A:404 , SER A:405 , VAL A:408 , HOH A:2722 , HOH A:2726BINDING SITE FOR RESIDUE NA A1420
2AC2SOFTWAREARG A:76 , HIS A:79 , SER A:365 , ILE A:367 , HOH A:2079BINDING SITE FOR RESIDUE NA A1421
3AC3SOFTWAREASP A:130 , HIS A:156 , TRP A:167 , GLU A:221 , TYR A:297 , GLU A:338 , TRP A:373 , ARG A:374 , GLN A:385 , HOH A:2098 , HOH A:2383 , HOH A:2486 , HOH A:2700 , HOH A:2701 , HOH A:2749 , HOH A:2750 , HOH A:2751 , HOH A:2752BINDING SITE FOR POLY-SACCHARIDE RESIDUES BMA A1422 THROUGH IFM A1423

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CD4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CD4)

(-) Exons   (0, 0)

(no "Exon" information available for 4CD4)

(-) 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
 aligned with B3PGI1_CELJU | B3PGI1 from UniProtKB/TrEMBL  Length:419

    Alignment length:367
                                    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       
         B3PGI1_CELJU    53 LPALIDTQATAETRALYRNLAKLRYKHLLFGHEDSLAYGVHWEGDMDRSDVRDVTGANPAVYGWELGGLELGHTANLDAVNFEKMQHWIKAGYSRGGVITISWHVFNPVSGGNSWDKTPAVHELIPGGARHATLKAYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTVHYLRDEKKLRNLIYAYSPDRSRIDMANFEAGYLYGYPGDAYVDIIGLDNYWDVGHEANTASADEQKAALTASLKQLVQIARSKGKIAALTETGNNRLTIDNFWTERLLGPISADADASEIAYVMVWRNANLAREKSEQFFAPFPGQATADDFKRFYQSEVVLFEDELPPLYR 419
               SCOP domains d4cd4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh...eeeeee....ee..ee.....hhhhhhhh....eeeee..hhhhh........hhhhhhhhhhhhhhh..eeeee.................hhhhhh....hhhhhhhhhhhhhhhhhh..ee.....ee...eeee.................hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh....hhhhh.ee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.ee.eeee........hhhhhhhhhhhhh..hhhhh.eeee......................hhhhhhhhhhh..eehhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cd4 A  53 LPALIDTQATAETRALYRNLAKLRYKHLLFGHEDSLAYGVHWEGDMDRSDVRDVTGANPAVYGWELGGLELGHTANLDAVNFEKMQHWIKAGYSRGGVITISWHVFNPVSGGNSWDKTPAVHELIPGGARHATLKAYLDTFVAFNEGLADVDAQGNKHYPPIIFRPWHEHNGDWFWWGKGHASEQDYIALWRFTVHYLRDEKKLRNLIYAYSPDRSRIDMANFEAGYLYGYPGDAYVDIIGLDNYWDVGHEANTASADEQKAALTASLKQLVQIARSKGKIAALTETGNNRLTIDNFWTERLLGPISADADASEIAYVMVWRNANLAREKSEQFFAPFPGQATADDFKRFYQSEVVLFEDELPPLYR 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  (0, 0)

(no "CATH Domain" information available for 4CD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CD4)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B3PGI1_CELJU | B3PGI1)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0016985    mannan endo-1,4-beta-mannosidase activity    Catalysis of the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.
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.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006080    substituted mannan metabolic process    The chemical reactions and pathways involving a mannan backbone composed of D-mannose unites, substituted with D-glucose and/or D-galactose units.

 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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IFM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 4cd4)
 

(-) 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
  4cd4
    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
  B3PGI1_CELJU | B3PGI1
    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)
  3.2.1.78
    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
  B3PGI1_CELJU | B3PGI1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3PGI1_CELJU | B3PGI1: 4cd5

(-) Related Entries Specified in the PDB File

4cd5 THE STRUCTURE OF GH26 BETA-MANNANASE CJMAN26C FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH MANMIM
4cd6 THE STRUCTURE OF GH113 BETA-MANNANASE AAMANA FROM ALICYCLOBACILLUS ACIDOCALDARIUS IN COMPLEX WITH MANIFG
4cd7 THE STRUCTURE OF GH113 BETA-MANNANASE AAMANA FROM ALICYCLOBACILLUS ACIDOCALDARIUS IN COMPLEX WITH MANIFG AND BETA-1,4-MANNOBIOSE
4cd8 THE STRUCTURE OF GH113 BETA-MANNANASE AAMANA FROM ALICYCLOBACILLUS ACIDOCALDARIUS IN COMPLEX WITH MANMIM