Structure Viewer: 7ubx

>   Structure details

Structure of a Pore Forming Fragment of Clostridium Difficile toxin a in complex with Vhh aa6

PDB7ubx
SpeciesCAMELIDAE
MethodX-RAY DIFFRACTION
Resolution1.81Å
Number of Fvs2
In complexTrue
Light chain typeNA
Has constant regionFalse
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>   Fv information

This PDB has 2 Fv(s).

>   D/-
Fv Details
Heavy chainD
Light chain
Heavy subgroupIGHV5
Light subgroupNA
SpeciesCAMELIDAE
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S D Y V M T W V R Q A P G K G P E W I A T I N T D G S T M R D D S T K G R F T I S R D N A K N T L Y L Q M T S L K P E D T A L Y Y C A R G R V I S A S A I R G A V R G P G T Q V T V S S

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nametoxin a
Antigen speciesCLOSTRIDIOIDES DIFFICILE
Antigen sequenceSMSLSIAATVASIVGIGAEVTIFLLPIAGISAGIPSLVNNELILHDKATSVVNYFNHLSESKKYGPLKTEDDKILVPIDDLVISEIDFNNNSIKLGTCNILAMEGGSGHTVTGNIDHFFSSPSISSHIPSLSIYSAIGIETENLDFSKKIMMLPNAPSRVFWWETGAVPGLRSLENDGTRLLDSIRDLYPGKFYWRFYAFFDYAITTLKPVYEDTNIKIKLDKDTRNFIMPTITTNEIRNKLSYSFDGAGGTYSLLLSSYPISTNINLSKDDLWIFNIDNEVREISIENGTIKKGKLIKDVLSKIDINKNKLIIGNQTIDFSGDIDNKDRYIFLTCELDDKISLIIEINLVAKSYSLLLSGDKNYLISNLSNTIEKINTLGLDSKNIAYNYTD

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2NTDGS
CDRH3GRVISASAIRGAV

>   C/-
Fv Details
Heavy chainC
Light chain
Heavy subgroupIGHV5
Light subgroupNA
SpeciesCAMELIDAE
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S D Y V M T W V R Q A P G K G P E W I A T I N T D G S T M R D D S T K G R F T I S R D N A K N T L Y L Q M T S L K P E D T A L Y Y C A R G R V I S A S A I R G A V R G P G T Q V T V S S

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nametoxin a
Antigen speciesCLOSTRIDIOIDES DIFFICILE
Antigen sequenceSMSLSIAATVASIVGIGAEVTIFLLPIAGISAGIPSLVNNELILHDKATSVVNYFNHLSESKKYGPLKTEDDKILVPIDDLVISEIDFNNNSIKLGTCNILAMEGGSGHTVTGNIDHFFSSPSISSHIPSLSIYSAIGIETENLDFSKKIMMLPNAPSRVFWWETGAVPGLRSLENDGTRLLDSIRDLYPGKFYWRFYAFFDYAITTLKPVYEDTNIKIKLDKDTRNFIMPTITTNEIRNKLSYSFDGAGGTYSLLLSSYPISTNINLSKDDLWIFNIDNEVREISIENGTIKKGKLIKDVLSKIDINKNKLIIGNQTIDFSGDIDNKDRYIFLTCELDDKISLIIEINLVAKSYSLLLSGDKNYLISNLSNTIEKINTLGLDSKNIAYNYTD

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2NTDGS
CDRH3GRVISASAIRGAV

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Chothia-numbered structure Download
IMGT-numbered structure Download
Non-annotated structure from the PDB Download
Summary file for this antibody Download

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]

Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link]

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