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(-) Description

Title :  CRYSTAL STRUCTURE OF TCDA-A2 BOUND TO A20.1 VHH AND A26.8 VHH
 
Authors :  T. Murase, L. Eugenio, M. Schorr, G. Hussack, J. Tanha, E. N. Kitova, J. S K. K. S. Ng
Date :  23 Oct 13  (Deposition) - 11 Dec 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Antibody-Antigen Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Murase, L. Eugenio, M. Schorr, G. Hussack, J. Tanha, E. N. Kitova, J. S. Klassen, K. K. Ng
Structural Basis For Antibody Recognition In The Receptor-Binding Domains Of Toxins A And B From Clostridium Difficile.
J. Biol. Chem. V. 289 2331 2014
PubMed-ID: 24311789  |  Reference-DOI: 10.1074/JBC.M113.505917

(-) Compounds

Molecule 1 - CELL WALL-BINDING REPEAT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-248
    Gene: HMPREF0219_0762, TCDA
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 525258
    Strain: 48489
 
Molecule 2 - A20.1 VHH
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VHH
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844
 
Molecule 3 - A26.8 VHH
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VHH
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NC1)

(-) Sites  (0, 0)

(no "Site" information available for 4NC1)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1C:29 -C:103
2D:29 -D:103
3E:22 -E:96
4F:22 -F:96

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val E:2 -Lys E:3
2Thr B:28 -Ala B:29
3Val F:2 -Lys F:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NC1)

(-) Exons   (0, 0)

(no "Exon" information available for 4NC1)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeee........eeeee..eeeeee...........ee.....eeeee..eeeee....ee..eeeee..eeeee.........eeee....eeeee..ee..eeeee..eeeeee...........ee.....eeeee..eeeee........eeeee..eeeee..........eeee....eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 A  44 YFNTNSIASTGYTIINDKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGRRYYFEPNTAIGANGYKIIDNKNFYFRNGLPQIGVFKGPNGFEYFAPANTDANNIDGQAIRYQNRFLHLLGNIYYFGNNSKAVTGWQTINGNMYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAP 258
                                ||  54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
                               48|                                                                                                                                                                                                                
                                50                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee.........eeeee..eeeee.........eeeee..eeeee........eeeee..eeeeee...........ee.....eeeee..eeeee........eeeee..eeeee.........eeeee..eeeeee..ee..eeeee..eeeeee...........ee.....eeeee..eeeee........eeeee..eeeee..........eeee....eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 B  12 TGMRTIDGKKYYFNTNTAEAATGWQTIDGKKYYFNTNTSIASTGYTIINDKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGRRYYFEPNTAIGANGYKIIDNKNFYFRNGLPQIGVFKGPNGFEYFAPANTDANNIDGQAIRYQNRFLHLLGNIYYFGNNSKAVTGWQTINGNMYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAPG 259
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        


Chain C from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4nc1c_ C: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.........eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 C   8 QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVAAGSSTGRTTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGTQVTVSS 130
                                    17        27        37        47        57        67        77        87        97       107       117       127   


Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4nc1d_ D: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee........eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee.........eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 D   8 QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVAAGSSTGRTTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGTQVTVS 129
                                    17        27        37        47        57        67        77        87        97       107       117       127  


Chain E from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4nc1e_ E: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeee.hhhhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee........hhhhh.ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 E   2 VKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFVAVISSTGTSTYYADSVKGRFTISRDNAKVTVYLQMNNLKREDTAVYFCAVNSQRTRLQDPNEYDYWGQGTQVTVSSH 125
                                    11        21        31        41        51        61        71        81        91       101       111       121    


Chain F from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4nc1f_ F: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...eeeeeeee.........eeeeee......eeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeee........hhhhh......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nc1 F   2 VKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFVAVISSTGTSTYYADSVKGRFTISRDNAKVTVYLQMNNLKREDTAVYFCAVNSQRTRLQDPNEYDYWGQGTQVTVSS 124
                                    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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NC1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NC1)

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  Sites
(no "Sites" information available for 4nc1)
 
  Cis Peptide Bonds
    Thr B:28 - Ala B:29   [ RasMol ]  
    Val E:2 - Lys E:3   [ RasMol ]  
    Val F:2 - Lys F:3   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        D5RWT1_CLODI | D5RWT1: 4nby 4nc0

(-) Related Entries Specified in the PDB File

2g7c TCDA-A2
4nbx
4nby
4nbz
4nc0
4nc2