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 :  BINDING DOMAIN OF BONT/A COMPLEXED WITH GANGLIOSIDE
 
Authors :  R. P. -A. Berntsson, L. M. Svensson, P. Stenmark
Date :  20 Oct 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Binding Domain, Lectin, Ganglioside Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Hamark, R. P. Berntsson, G. Masuyer, L. M. Henriksson, R. Gustafsson, P. Stenmark, G. Widmalm
Glycans Confer Specificity To The Recognition Of Gangliosid Receptors By Botulinum Neurotoxin A.
J. Am. Chem. Soc. V. 139 218 2017
PubMed-ID: 27958736  |  Reference-DOI: 10.1021/JACS.6B09534

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
    Chains: A
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: BOTA, ATX, BNA
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: BONT/A,BONTOXILYSIN-A,BOTOX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
3SIA2Ligand/IonO-SIALIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:1266 , NGA A:1303 , HOH A:1413binding site for Poly-Saccharide residues GAL A 1301 through SIA A 1302
2AC2SOFTWARELEU A:928 , SER A:1050 , ASN A:1052 , TYR A:1117 , VAL A:1202 , GLU A:1203 , PHE A:1252 , HIS A:1253 , SER A:1264 , TRP A:1266 , GAL A:1301 , SIA A:1302 , HOH A:1445 , HOH A:1559 , HOH A:1573 , HOH A:1627 , HOH A:1641binding site for Poly-Saccharide residues ASN A 1051 through SIA A 1305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TPC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:1138 -Pro A:1139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TPC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TPC)

(-) Exons   (0, 0)

(no "Exon" information available for 5TPC)

(-) 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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..eeee......eeee....ee.......eeee......eeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhh...................eeee......eee..........eee....eeee...eeee.......eeeee..............eeeeeeee..eeeeee........eee.eeehhhhh.....eeeeee.........eeeeee.....eeeeeeeeee..eeeeeee.........hhhhhhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tpc A  873 HMDTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPLQ 1297
                                   882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292
   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 5TPC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TPC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TPC)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:1138 - Pro A:1139   [ RasMol ]  
 

(-) 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
  5tpc
    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
  BXA1_CLOBO | P10845
    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)
  3.4.24.69
    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
  BXA1_CLOBO | P10845
    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
        BXA1_CLOBO | P10845: 1uee 1xtf 1xtg 2ilp 2ima 2imb 2imc 2ise 2isg 2ish 2nyy 2nz9 2vu9 2vua 2w2d 3bok 3bon 3boo 3bta 3bwi 3c88 3c89 3c8a 3c8b 3dda 3ddb 3ds9 3fuo 3v0a 3v0b 3v0c 3zur 3zus 4ej5 4el4 4elc 4hev 4iqp 4jra 4zjx 5jlv 5jmc 5tpb 5vgv 5vgx

(-) Related Entries Specified in the PDB File

2vu9 2VU9 CONTAINS THE SAME PROTEIN COMPLEXED TO GT1B