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(-)Asym./Biol. Unit
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(-) Description

Title :  CLOSTRIDIUM DIFFICILE TOXIN B CROP DOMAIN IN COMPLEX WITH FAB DOMAINS OF NEUTRALIZING ANTIBODY BEZLOTOXUMAB
 
Authors :  P. Orth, L. Xiao, L. D. Hernandez, P. Reichert, P. Sheth, M. Beaumont, N. G. Ermakov, E. Dinunzio, F. Racine, J. Karczewski, S. Secore, R. N. Ing T. Mayhood, C. Strickland, A. G. Therien
Date :  20 Nov 13  (Deposition) - 21 May 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,H,I,L,M
Keywords :  Bezlotoxumab, Human Antibody, Fab, Crop Domain, Cytotoxin, Short Repeat, Long Repeat, Tcdb, Receptor Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Orth, L. Xiao, L. D. Hernandez, P. Reichert, P. R. Sheth, M. Beaumont X. Yang, N. Murgolo, G. Ermakov, E. Dinunzio, F. Racine, J. Karczewski S. Secore, R. N. Ingram, T. Mayhood, C. Strickland, A. G. Therien
Mechanism Of Action And Epitopes Of Clostridium Difficile Toxin B-Neutralizing Antibody Bezlotoxumab Revealed By X-Ra Crystallography.
J. Biol. Chem. V. 289 18008 2014
PubMed-ID: 24821719  |  Reference-DOI: 10.1074/JBC.M114.560748

(-) Compounds

Molecule 1 - TOXIN B
    Chains: A
    Fragment: CROP DOMAIN(UNP RESIDUES 1834-2099)
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 1496
 
Molecule 2 - BEZLOTOXUMAB HEAVY CHAIN
    Chains: H, I
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - BEZLOTOXUMAB LIGHT CHAIN
    Chains: L, M
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : AHILM

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NP4)

(-) Sites  (0, 0)

(no "Site" information available for 4NP4)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:202
3I:22 -I:96
4I:146 -I:202
5L:23 -L:89
6L:135 -L:195
7M:23 -M:89
8M:135 -M:195

(-) Cis Peptide Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1Trp H:102 -Gly H:103
2Phe H:152 -Pro H:153
3Glu H:154 -Pro H:155
4Val I:76 -Asn I:77
5Trp I:102 -Gly I:103
6Phe I:152 -Pro I:153
7Glu I:154 -Pro I:155
8Asn I:161 -Ser I:162
9Ser L:7 -Pro L:8
10Tyr L:92 -Gly L:93
11Tyr L:141 -Pro L:142
12Ser M:7 -Pro M:8
13Tyr M:141 -Pro M:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NP4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NP4)

(-) 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:271
                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeee....ee..eeeee..eeeeee.....ee..eeeee..eeeee........eeee....eeeee...........ee....eeeee..eeeeee...ee..eeeee..eeeee.........eeeee..eeeee........eeeee..eeeee........eeeee..eeeee........eeeee..eeeeee...........ee....eeeee..eeeee........eeee.....eeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4np4 A 1834 GLIYINDSLYYFKPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENLEGEAIDFTGKLIIDENIYYFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAVVGWKDLEDGSKYYFDEDTAEAYILEHHH 2104
                                  1843      1853      1863      1873      1883      1893      1903      1913      1923      1933      1943      1953      1963      1973      1983      1993      2003      2013      2023      2033      2043      2053      2063      2073      2083      2093      2103 


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee........eeee.....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.....eeeeeeeeee.....eee.........eee...ee.....eeeeeeeeehhhhh....eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4np4 H    1 EVQLVQSGAEVKKSGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIFYPGDSSTRYSPSFQGQVTISADKSVNTAYLQWSSLKASDTAMYYCARRRNWGNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  146       156       166       176       186       196       206       216     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                141                                                                                


Chain I from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee........eeee.....eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee..........eeeeeeeeeee.....eee.........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4np4 I    1 EVQLVQSGAEVKKSGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIFYPGDSSTRYSPSFQGQVTISADKSVNTAYLQWSSLKASDTAMYYCARRRNWGNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee.....eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeeee....eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4np4 L    1 EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSTWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee.....eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4np4 M    1 EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSTWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4NP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NP4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Sites
(no "Sites" information available for 4np4)
 
  Cis Peptide Bonds
    Asn I:161 - Ser I:162   [ RasMol ]  
    Glu H:154 - Pro H:155   [ RasMol ]  
    Glu I:154 - Pro I:155   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Phe I:152 - Pro I:153   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser M:7 - Pro M:8   [ RasMol ]  
    Trp H:102 - Gly H:103   [ RasMol ]  
    Trp I:102 - Gly I:103   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
    Tyr L:92 - Gly L:93   [ RasMol ]  
    Tyr M:141 - Pro M:142   [ RasMol ]  
    Val I:76 - Asn I:77   [ RasMol ]  
 

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UniProtKB/Swiss-Prot
        TOXB_CLODI | P18177: 2bvl 2bvm 4nc2 5uqm 5uqn 5uqt

(-) Related Entries Specified in the PDB File

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