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

(-) Description

Title :  CRYSTAL STRUCTURE OF A HEMAGGLUTININ COMPONENT (HA1) FROM TYPE C CLOSTRIDIUM BOTULINUM
 
Authors :  K. Inoue, M. Sobhany, T. R. Transue, K. Oguma, L. C. Pedersen, M. Negishi
Date :  08 Sep 03  (Deposition) - 20 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Clostridium Botulinum, Hemagglutinin, Ha1, Trefoil, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Inoue, M. Sobhany, T. R. Transue, K. Oguma, L. C. Pedersen, M. Negishi
Structural Analysis By X-Ray Crystallography And Calorimetry Of A Haemagglutinin Component (Ha1) Of The Progenitor Toxin From Clostridium Botulinum.
Microbiology V. 149 3361 2003
PubMed-ID: 14663070  |  Reference-DOI: 10.1099/MIC.0.26586-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HA1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T-3
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HEMAGGLUTININ COMPONENT HA1
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM BOTULINUM D PHAGE
    Organism Taxid: 29342

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:57 , TYR A:94 , ASN B:98 , SER B:101 , ASN B:103 , PHE B:136 , HOH B:742BINDING SITE FOR RESIDUE EDO B 701
2AC2SOFTWAREASN A:98 , SER A:101 , ASN A:103 , PHE A:136 , GLN B:57 , TYR B:94BINDING SITE FOR RESIDUE EDO A 702
3AC3SOFTWAREGLN A:97 , TYR A:99 , ARG A:102 , HOH A:768 , HOH A:971 , GLN B:97 , TYR B:99 , ARG B:102BINDING SITE FOR RESIDUE EDO A 703
4AC4SOFTWAREASP B:28 , TRP B:38 , ASN B:45 , GLN B:46 , GLN B:157 , HOH B:753 , HOH B:793BINDING SITE FOR RESIDUE EDO B 704
5AC5SOFTWAREHOH A:1052 , LYS B:166 , LEU B:168 , TRP B:176 , ARG B:183BINDING SITE FOR RESIDUE EDO B 705
6AC6SOFTWAREASP A:28 , ILE A:30 , LEU A:41 , ASN A:45 , HOH A:775 , HOH B:907BINDING SITE FOR RESIDUE EDO A 706
7AC7SOFTWAREILE A:70 , ASP A:85 , HOH A:955 , HOH A:1020 , HOH B:727BINDING SITE FOR RESIDUE EDO A 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QXM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:75 -Pro A:76
2Ala B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 26)

Asymmetric/Biological Unit (13, 26)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_HA33_CLOBO_001 *N22SHA33_CLOBO  ---  ---A/BN22S
02UniProtVAR_HA33_CLOBO_002 *K60THA33_CLOBO  ---  ---A/BK60T
03UniProtVAR_HA33_CLOBO_003 *N74DHA33_CLOBO  ---  ---A/BN74D
04UniProtVAR_HA33_CLOBO_004 *N98DHA33_CLOBO  ---  ---A/BN98D
05UniProtVAR_HA33_CLOBO_005 *I106LHA33_CLOBO  ---  ---A/BI106L
06UniProtVAR_HA33_CLOBO_006 *I120THA33_CLOBO  ---  ---A/BI120T
07UniProtVAR_HA33_CLOBO_007 *M125IHA33_CLOBO  ---  ---A/BM125I
08UniProtVAR_HA33_CLOBO_008 *S131NHA33_CLOBO  ---  ---A/BS131N
09UniProtVAR_HA33_CLOBO_009 *S133NHA33_CLOBO  ---  ---A/BS133N
10UniProtVAR_HA33_CLOBO_010 *I187LHA33_CLOBO  ---  ---A/BI187L
11UniProtVAR_HA33_CLOBO_011 *I187THA33_CLOBO  ---  ---A/BI187T
12UniProtVAR_HA33_CLOBO_012 *I262THA33_CLOBO  ---  ---A/BI262T
13UniProtVAR_HA33_CLOBO_013 *H267NHA33_CLOBO  ---  ---A/BH267N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.HA33_CLOBO12-140
 
180-284
 		  4A:12-140
B:12-140
A:180-284
B:180-284

(-) Exons   (0, 0)

(no "Exon" information available for 1QXM)

(-) 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:283
 aligned with HA33_CLOBO | P46084 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           HA33_CLOBO     4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
               SCOP domains d1qxma1 A:4-148 Hemagglutinin component Ha1                                                                                                      d1qxma2 A:149-286 Hemagglutinin component Ha1                                                                                              SCOP domains
               CATH domains 1qxmA01 A:4-141  [code=2.80.10.50, no name defined]                                                                                       1qxmA02 A:142-286  [code=2.80.10.50, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.....eeeee.....eeeee...hhhh.eeeeee....eeeeee......eeee......eeee....hhhh.eeeee......eeeee.....eeeee.....eeeee...hhhh.eeeeehhhhhhh.eeeeeee......eeee......eeee....hhhh.eeeeee....eeeeee....eeeee.......eeee....hhhh.eeeeee..eeeeeeeee.....eeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------S-------------------------------------T-------------D-----------------------D-------L-------------T----I-----N-N-----------------------------------------------------L--------------------------------------------------------------------------T----N------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------RICIN_B_LECTIN  PDB: A:12-140 UniProt: 12-140                                                                                    ---------------------------------------RICIN_B_LECTIN  PDB: A:180-284 UniProt: 180-284                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qxm A   4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with HA33_CLOBO | P46084 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           HA33_CLOBO     4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
               SCOP domains d1qxmb1 B:4-148 Hemagglutinin component Ha1                                                                                                      d1qxmb2 B:149-286 Hemagglutinin component Ha1                                                                                              SCOP domains
               CATH domains 1qxmB01 B:4-141  [code=2.80.10.50, no name defined]                                                                                       1qxmB02 B:142-286  [code=2.80.10.50, no name defined]                                                                                             CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RicinB_lectin_2-1qxmB01 B:182-284                                                                      -- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RicinB_lectin_2-1qxmB02 B:182-284                                                                      -- Pfam domains (2)
         Sec.struct. author ..........eeeeee.....eeeee.....eeeee...hhhh.eeeeee....eeeeee......eeee......eeee....hhhh.eeeee......eeeee.....eeeee.....eeeee...hhhh.eeeeehhhhhhh.eeeeeee......eeee......eeee....hhhh.eeeeee....eeeeee.....eeee.......eeee....hhhh.eeeeee..eeeeeeeee..eeeeeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------S-------------------------------------T-------------D-----------------------D-------L-------------T----I-----N-N-----------------------------------------------------L--------------------------------------------------------------------------T----N------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------RICIN_B_LECTIN  PDB: B:12-140 UniProt: 12-140                                                                                    ---------------------------------------RICIN_B_LECTIN  PDB: B:180-284 UniProt: 180-284                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qxm B   4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HA33_CLOBO | P46084)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

 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
    EDO  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:75 - Pro A:76   [ RasMol ]  
    Ala B:75 - Pro B:76   [ 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
  1qxm
    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
  HA33_CLOBO | P46084
    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
  HA33_CLOBO | P46084
    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
        HA33_CLOBO | P46084: 2e4m 3ah1 3ah2 3ah4 3aj5 3aj6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QXM)