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 :  CLOSTRIDIUM BOTULINUM SEROTYPE A LIGHT CHAIN INHIBITED BY ADAMANTANE HYDROXAMATE
 
Authors :  N. R. Silvaggi, K. N. Allen
Date :  04 Oct 12  (Deposition) - 23 Jan 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zn2+-Dependent Metalloprotease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Silhar, N. R. Silvaggi, S. Pellett, E. A. Johnson, K. N. Allen, K. D. Janda
Evaluation Of Adamantane Hydroxamates As Botulinum Neurotoxin Inhibitors: Synthesis, Crystallography, Modeling Kinetic And Cellular Based Studies.
Bioorg. Med. Chem. V. 21 1344 2013
PubMed-ID: 23340139  |  Reference-DOI: 10.1016/J.BMC.2012.12.001

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
    ChainsA, B
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15-LC425
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePET-15B
    FragmentUNP RESIDUES 1-425
    GeneBOTA, ATX, BNA
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    SynonymBONT/A, BONTOXILYSIN-A, BOTOX

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AXM2Ligand/IonN-HYDROXY-2-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]ACETAMIDE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AXM1Ligand/IonN-HYDROXY-2-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]ACETAMIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AXM1Ligand/IonN-HYDROXY-2-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]ACETAMIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:223 , HIS A:227 , GLU A:262 , AXM A:502BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREILE A:161 , PHE A:163 , PHE A:194 , HIS A:223 , GLU A:224 , HIS A:227 , GLU A:262 , TYR A:366 , ZN A:501 , HOH A:618BINDING SITE FOR RESIDUE AXM A 502
3AC3SOFTWAREHIS B:223 , HIS B:227 , GLU B:262 , AXM B:502BINDING SITE FOR RESIDUE ZN B 501
4AC4SOFTWAREILE B:161 , PHE B:163 , PHE B:194 , HIS B:223 , GLU B:224 , HIS B:227 , GLU B:262 , TYR B:366 , ZN B:501 , HOH B:636BINDING SITE FOR RESIDUE AXM B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HEV)

(-) 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4heva_ A: Botulinum neurotoxin                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................eeeee......eeeeeee..eeee...........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee.hhh.eeee........eee..eeee.........eeee................eeee....eeeeeee......eeee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhh.ee.....ee.hhhhhhhhhhhhhh..hhhhhhhhhh.............eee.........................hhhhh...hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hev A  -9 SSGLVPRGSHMQFVNKQFNYKDPVNGVDIAYIKIPQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLELGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLK 417
                                     0        10        20    ||  33        43        53        70        80        90       100       110       120       130       140       150       160       170       180       190       200||     216       226       236     ||260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       
                                                             25|                               62|                                                                                                                                201|                               242|                                                                                                                                                                
                                                              29                                70                                                                                                                                 208                                257                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4hevb_ B: Botulinum neurotoxin                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................eeeee......eeeeeee..eeeeeee........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee..hhh.eeee........eee..eeeee........eeee................eeee....eeeeee.....eee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhh..ee.....ee.hhhhhhhhhhhhhh..hhhhhhhhhh.............eee.................................hhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hev B  -9 SSGLVPRGSHMQFVNKQFNYKDPVNGVDIAYIKIPQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKL 416
                                     0        10        20    ||  33        43        53        70        80        90       100       110       120       130       140       150       160       170       180       190       209       219       229       239  ||   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413   
                                                             25|                               62|                                                                                                                              199|                              242|                                                                                                                                                               
                                                              29                                70                                                                                                                               209                               257                                                                                                                                                               

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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
    AXM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hev)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4hev
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BXA1_CLOBO | P10845
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.69
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BXA1_CLOBO | P10845
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BXA1_CLOBO | P108451uee 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 4iqp 4jra 4zjx 5jlv 5jmc 5tpb 5tpc 5vgv 5vgx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HEV)