Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH 1,6-MANIFG
 
Authors :  A. J. Thompson, G. Speciale, J. Iglesias-Fernandez, Z. Hakki, T. Belz, A. Cartmell, R. J. Spears, J. Stepper, H. J. Gilbert, C. Rovira, S. J. Wi G. J. Davies
Date :  27 Oct 14  (Deposition) - 25 Mar 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Glycoside Hydrolase, Gh76, Cazy, Mannan, Enzyme-Carbohydrate Interaction, Glycosidase Inhibition, Transition State (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Thompson, G. Speciale, J. Iglesias-Fernandez, Z. Hakki, T. Belz A. Cartmell, R. J. Spears, E. Chandler, M. J. Temple, J. Stepper, H. J. Gilbert, C. Rovira, S. J. Williams, G. J. Davies
Evidence For A Boat Conformation At The Transition State Of Gh76 Alpha-1, 6-Mannanases- Key Enzymes In Bacterial And Fungal Mannoprotein Metabolism
Angew. Chem. Int. Ed. Engl. V. 54 5378 2015
PubMed-ID: 25772148  |  Reference-DOI: 10.1002/ANIE.201410502

(-) Compounds

Molecule 1 - ALPHA-1,6-MANNANASE
    Atcc: 29101
    Chains: A, B
    EC Number: 3.2.1.101
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: TUNER
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397
    Strain: TN31

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2IFM2Ligand/Ion5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
3MAN2Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2IFM1Ligand/Ion5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
3MAN1Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2IFM1Ligand/Ion5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
3MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:49 , TRP B:53 , GLU B:97 , GLN B:101 , HOH B:2025 , HOH B:2122BINDING SITE FOR RESIDUE EDO B 402
2AC2SOFTWARETRP A:73 , ASP A:124 , ASP A:125 , TRP A:128 , TRP A:172 , ASN A:181 , CYS A:183 , ASP A:228 , TYR A:243 , ASP A:294 , HOH A:2189 , HOH A:2268 , HOH A:2269 , HOH A:2324 , HOH A:2479 , HOH A:2481BINDING SITE FOR POLY-SACCHARIDE RESIDUES IFM A 400 THROUGH MAN A 401
3AC3SOFTWARETRP B:73 , ASP B:124 , ASP B:125 , TRP B:128 , TRP B:172 , ASN B:181 , CYS B:183 , ASP B:228 , TYR B:243 , ASP B:294 , HOH B:2184 , HOH B:2251 , HOH B:2252 , HOH B:2305 , HOH B:2458 , HOH B:2459BINDING SITE FOR POLY-SACCHARIDE RESIDUES IFM B 400 THROUGH MAN B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D4D)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:290 -Pro A:291
2Ser B:24 -Ser B:25
3Gly B:290 -Pro B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D4D)

(-) Exons   (0, 0)

(no "Exon" information available for 4D4D)

(-) Sequences/Alignments

Asymmetric 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4d A  39 SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGQGTYESWSSAAAVQALNG 374
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     ||361       371   
                                                                                                                                                                                                                                                                                                                                                     354|                
                                                                                                                                                                                                                                                                                                                                                      358                


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhee....ee..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee...ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4d B  19 HHHHHSSSDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQHTSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPAAQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVPDATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNYEGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAWSHQNSDHIVDGNWAGQLLSGTYESWSSAAAVQALNG 374
                                  ||41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371   
                                 25|                                                                                                                                                                                                                                                                                                                                               
                                  39
   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 4D4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D4D)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IFM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:290 - Pro A:291   [ RasMol ]  
    Gly B:290 - Pro B:291   [ RasMol ]  
    Ser B:24 - Ser B:25   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4d4d
    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
  Q9Z4P9_BACCI | Q9Z4P9
    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)
  3.2.1.101
    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
  Q9Z4P9_BACCI | Q9Z4P9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9Z4P9_BACCI | Q9Z4P9: 4boj 4bok 4d4a 4d4b 4d4c 5agd

(-) Related Entries Specified in the PDB File

4d4a STRUCTURE OF THE CATALYTIC DOMAIN (BCGH76) OF THE BACILLUS CIRCULANS GH76 ALPHA MANNANASE, AMAN6.
4d4b THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH MSMSME
4d4c THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH 1,6-MANDMJ
5agd AN INACTIVE (D125N) VARIANT OF THE CATALYTIC DOMAIN, BCGH76, OF BACILLUS CIRCULANS AMAN6 IN COMPLEX WITH ALPHA-1,6-MANNOPENTAOSE