Structure Viewer: 5f7n

>   Structure details

Blood Group antigen Binding adhesin Baba of Helicobacter Pylori Strain 17875 in complex with Blood Group a Lewis B Pentasaccharide

PDB5f7n
SpeciesHELICOBACTER PYLORI
MethodX-RAY DIFFRACTION
Resolution2.28Å
Number of Fvs2
In complexTrue
Light chain type
Has constant regionFalse
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>   Fv information

This PDB has 2 Fv(s).

>   D/-
Fv Details
Heavy chainD
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesHELICOBACTER PYLORI
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 98 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G S I F S G N V M G W Y R Q A P G K L R E W V A A I T P Q G V P N Y A D S V K G R F T I S R D N A K N M L Y L Q M S S L K P E D T A L Y Y C N R L P N Y R S W G Q G T Q V T V S S

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nameadhesin binding fucosylated histo-blood group antigen
Antigen speciesHELICOBACTER PYLORI
Antigen sequenceASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH

CDR Sequences (chothia definition)
CDRH1GSIFSGN
CDRH2TPQGV
CDRH3LPNYRS

>   C/-
Fv Details
Heavy chainC
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesHELICOBACTER PYLORI
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 98 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G S I F S G N V M G W Y R Q A P G K L R E W V A A I T P Q G V P N Y A D S V K G R F T I S R D N A K N M L Y L Q M S S L K P E D T A L Y Y C N R L P N Y R S W G Q G T Q V T V S S

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameadhesin binding fucosylated histo-blood group antigen
Antigen speciesHELICOBACTER PYLORI
Antigen sequenceASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH

CDR Sequences (chothia definition)
CDRH1GSIFSGN
CDRH2TPQGV
CDRH3LPNYRS

>   Downloads

Additional links and files for download: see help for more details.

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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