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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF HA70 (HA3) SUBCOMPONENT OF CLOSTRIDIUM BOTULINUM TYPE C PROGENITOR TOXIN IN COMPLEX WITH ALPHA 2-6-SIALYLLACTOSAMINE
 
Authors :  S. Yamashita, H. Yoshida, T. Tonozuka, A. Nishikawa, S. Kamitori
Date :  12 Apr 12  (Deposition) - 06 Jun 12  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Carbohydrate/Sugar Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, H. Yoshida, N. Uchiyama, Y. Nakakita, S. Nakakita, T. Tonozuka, K. Oguma, A. Nishikawa, S. Kamitori
Carbohydrate Recognition Mechanism Of Ha70 From Clostridium Botulinum Deduced From X-Ray Structures In Complexes With Sialylated Oligosaccharides
Febs Lett. V. 586 2404 2012
PubMed-ID: 22684008  |  Reference-DOI: 10.1016/J.FEBSLET.2012.05.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMAGGLUTININ COMPONENTS HA-22/23/53
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-CRI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HA22-23(HA3A)
    Gene: HA-70
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: HEMAGGLUTININ COMPONENTS HA70, HA3
 
Molecule 2 - HEMAGGLUTININ COMPONENTS HA-22/23/53
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-CRI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HA53(HA3B)
    Gene: HA-70
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: HEMAGGLUTININ COMPONENTS HA70, HA3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2MRD5Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1GAL3Ligand/IonBETA-D-GALACTOSE
2MRD15Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:102 , SER A:104 , HOH A:427 , SER B:243 , VAL B:293BINDING SITE FOR RESIDUE MRD A 301
2AC2SOFTWAREASP A:58 , LEU A:59 , GLY A:100 , GLU A:102 , PRO B:247BINDING SITE FOR RESIDUE MRD A 302
3AC3SOFTWARELYS A:161 , PHE A:165 , HOH A:451 , ILE B:368 , ILE B:369BINDING SITE FOR RESIDUE MRD A 303
4AC4SOFTWAREILE B:264 , TYR B:269 , ASN B:317 , ASN B:374 , SER B:376BINDING SITE FOR RESIDUE MRD B 704
5AC5SOFTWAREASN A:50 , HOH A:411 , GLU B:294 , PRO B:297 , LYS B:300 , ILE B:302 , ASP B:341BINDING SITE FOR RESIDUE MRD B 705
6AC6SOFTWAREASN B:320 , ARG B:460 , SER B:461 , ASP B:462 , ASP B:513 , ASN B:514 , TYR B:522 , TYR B:523 , THR B:524 , ARG B:525 , HOH B:801 , HOH B:802 , HOH B:803 , HOH B:804BINDING SITE FOR LINKED RESIDUES B 701 TO 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EN9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:423 -Pro B:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EN9)

(-) Exons   (0, 0)

(no "Exon" information available for 4EN9)

(-) 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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeee.........eeeee...eeeeeee........eee.....hhhhhhhhhhhhh.hhhhhh....eeeeeee.....eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeee................ee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en9 A  15 SINNVNLADGNYVVNRGDGWILSRQNQNLGGNISNNGCTAIVGDLRIRETATPYYYPTASFNEEYIKNNVQNVFANFTEASEIPIGFEFSKTAPSNKSLYMYLQYTYIRYEIIKVLQNTVTERAVLYVPSLGYVKSIEFNSEEQIDKNFYFTSQDKCILNEKFIYKKIDD 184
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184


Chain B from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eee.....eeeeeee....eeeeee.........eeee......hhhhhhhhhhhhhh.........eeeeeee......eeeeee..eeeeeeeeee..eeeeeeeeeee...eeeeee.................eee......eeeee.....eeee.......eeeee.hhhhhh..eeeee.....eeeeee........eeeee.......ee..........eeeeeee.......eeeeeee.....eeeee.........eeeeeee.hhhhhhh.eeeee..........eeeee......eeeeeee.........eeeeeeee...eeeeeeeeee......eeeeeeee.........eeee...eeeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4en9 B 204 QTILPYPNGLYVINKGDGYMRTNDKDLIGTLLIESSTSGSIIQPRLRNTTRPLFNTSNPTIFSQEYTEARLNDAFNIQLFNTSTTLFKFVEEAPTNKNISMKVYNTYEKYELINYQNGNIDDKAEYYLPSLGKCEVSDAPSPQAPVVETPVDQDGFIQTGPNENIIVGVINPSENIEEISTPIPDDYTYNIPTSIQNNACYVLFKVNTTGVYKITTKNNLPPLIIYEAIGSSNRNMNSNNLSNDNIKAIKYITGLNRSDAKSYLIVSLFKDKNYYIRIPQISSSTTSQLIFKRELGNISDLADSTVNILDNLNTSGTHYYTRQSPDVGNYISYQLTIPGDFNNIASSIFSFRTRNNQGIGTLYRLTESINGYNLITINNYSDLLNNVEPISLLNGATYIFRVKVTELNNYNIIFDAYRNS 623
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623
   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 4EN9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EN9)

(-) 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
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu B:423 - Pro B:424   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4en9
    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
  HA70_CLOBO | P46085
    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)
  (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
  HA70_CLOBO | P46085
    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
        HA70_CLOBO | P46085: 2zoe 2zs6 4en6 4en7 4en8

(-) Related Entries Specified in the PDB File

2zoe THE SAME SUBCOMPONENT IN COMPLEX WITH N-ACETYLNEURAMIC ACID
2zs6 THE SAME SUBCOMPONENT WITHOUT LIGAND
4en6 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-3- SIALYLLACTOSE
4en7 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-3- SIALYLLACTOSAMINE
4en8 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-6- SIALYLLACTOSE