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

(-) Description

Title :  COMPLEX OF SHIGA TOXIN 2E WITH A NEUTRALIZING SINGLE-DOMAIN ANTIBODY
 
Authors :  A. W. H. Lo, K. Moonens, M. De Kerpel, L. Brys, E. Pardon, H. Remaut, H. De
Date :  18 Feb 14  (Deposition) - 30 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K
Keywords :  Nanobody, Toxin, Complex, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. W. Lo, K. Moonens, M. De Kerpel, L. Brys, E. Pardon, H. Remaut, H. De Greve
The Molecular Mechanism Of Shiga Toxin Stx2E Neutralization By A Single-Domain Antibody Targeting The Cell Receptor-Binding Domain.
J. Biol. Chem. V. 289 25374 2014
PubMed-ID: 25053417  |  Reference-DOI: 10.1074/JBC.M114.566257

(-) Compounds

Molecule 1 - SHIGA TOXIN 2E, SUBUNIT A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - SHIGA TOXIN 2E, SUBUNIT B
    Chains: B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: STXB2E, ORF, STX2E B, STX2EB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SLT-IIEB, SHIGA TOXIN 2 VARIANT E B-SUBUNIT, SHIGA TOXIN 2B SUBUNIT, SHIGA TOXIN 2E B, SHIGA TOXIN 2E SUBUNIT B, SHIGA-LIKE TOXIN 2B-SUBUNIT, SHIGA-LIKE TOXIN IIE VARIANT SUBUNIT B, SLT-IIVB, VEROTOXIN 2E SUBUNIT B
 
Molecule 3 - NANOBODY 1, ANTI-F4+ETEC BACTERIA VHH VARIABLE REGION
    Chains: G, H, I, J, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric/Biological Unit : ABCDEFGHIJK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4P2C)

(-) Sites  (0, 0)

(no "Site" information available for 4P2C)

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:241 -A:260
2B:3 -B:56
3C:3 -C:56
4D:3 -D:56
5E:3 -E:56
6F:3 -F:56
7G:22 -G:95
8H:22 -H:95
9I:22 -I:95
10J:22 -J:95
11K:22 -K:95

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:45 -Pro A:46
2Gly K:106 -Pro K:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4P2C)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhheeeeeeee....eeeee.......eeeeee.............eeeee.....eeeeee....eeee.hhhh.......ee........hhhhhhhh.......eehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhh....eeee..eee.hhhhhh....ee.............eeee..eeee...hhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2c A   1 QEFTIDFSTQQSYVSSLNSIRTAISTPLEHISQGATSVSVINHTPPGSYISVGIRGLDVYQERFDHLRLIIERNNLSVAGFVNTTTNTFYRFSDFAHISLPGVTTISMTTDSSYTTPQRVAALERSGMQVSRHSLVSSYLALMEFSGNTMTREASRAVLRFVTVTAQALRFRQIQREFRQALSETAPVYTMTPEDVDLTLNWGRISNVLPEYRGEAGVRVGRISFNNISAILGTVAVILNCHECQITGDRPVIKITNTLWESNTAAAFLNRKSQSLYTTG 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 ||    266       276       286       296
                                                                                                                                                                                                                                                                           242|                                     
                                                                                                                                                                                                                                                                            259                                     


Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eee.....eeeee..eeeee...hhhhhhhhhhhh..eeeee.......ee...eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p2c B   1 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  68
                                    10        20        30        40        50        60        


Chain C from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhh..eeeee.......eee.eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p2c C   1 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  68
                                    10        20        30        40        50        60        


Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eee.....eeeee..eeeee...hhhhhhhhhhhh..eeeee.......ee..eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p2c D   1 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  68
                                    10        20        30        40        50        60        


Chain E from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhh..eeeee.......ee...eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p2c E   1 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  68
                                    10        20        30        40        50        60        


Chain F from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eee.....eeeee..eeeee...hhhhhhhhhhhh..eeeee.......ee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4p2c F   1 ADCAKGKIEFSKYNEDNTFTVKVSGREYWTNRWNLQPLLQSAQLTGMTVTIISNTCSSGSGFAQVKFN  68
                                    10        20        30        40        50        60        


Chain G from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeeehhhhhh.eeeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..........eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2c G   1 QVQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain H from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeehhhhhh.eeeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..........eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p2c H   2 VQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVS 121
                                    11        21        31        41        51        61        71        81        91       101       111       121


Chain I from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeehhhhhh.eeeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p2c I   2 VQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVS 121
                                    11        21        31        41        51        61        71        81        91       101       111       121


Chain J from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeehhhhhh.eeeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..........eee....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2c J   2 VQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVSSHHHHHH 128
                                    11        21        31        41        51        61        71        81        91       101       111       121       


Chain K from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeehhhhhh.eeeeeeee......eeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........eee....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p2c K   2 VQLQESGGGLVQAGGSLRLSCAVSGSIFRLSTMGWYRQAPGKQREFVASITSYGDTNYRDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNANIEAGTYYGPGRDYWGQGTQVTVS 121
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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 4P2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P2C)

(-) Gene Ontology  (5, 5)

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
(no "Ligands, Modified Residues, Ions" information available for 4p2c)
 
  Sites
(no "Sites" information available for 4p2c)
 
  Cis Peptide Bonds
    Gly K:106 - Pro K:107   [ RasMol ]  
    Pro A:45 - Pro A:46   [ 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 ](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
  4p2c
    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
  Q47644_ECOLX | Q47644
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q7WUF4_ECOLX | Q7WUF4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  R9VYW2_LAMGL | R9VYW2
    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)
  (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
  Q47644_ECOLX | Q47644
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q7WUF4_ECOLX | Q7WUF4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  R9VYW2_LAMGL | R9VYW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q47644_ECOLX | Q47644: 1qoh 2bos
        R9VYW2_LAMGL | R9VYW2: 4wen

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P2C)