Structure Viewer: 3gbm

>   Structure details

Crystal Structure of Fab Cr6261 in complex with a H5N1 influenza Virus Hemagglutinin.

PDB3gbm
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.7Å
Number of Fvs2
In complexTrue
Light chain typeLambda
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGLV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 52A 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G A E V K K P G S S V K V S C K A S G G P F R S Y A I S W V R Q A P G Q G P E W M G G I I P I F G T T K Y A P K F Q G R V T I T A D D F A G T V Y M E L S S L R S E D T A M Y Y C A K H M G Y Q V R E T M D V W G K G T T V T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 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 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q P P S V S A A P G Q K V T I S C S G S S S N I G N D Y V S W Y Q Q L P G T A P K L L I Y D N N K R P S G I P D R F S G S K S G T S A T L G I T G L Q T G D E A N Y Y C A T W D R R P T A Y V V F G G G T K L T V L

Antigen Details
Antigen chainsB,A
Antigen typeprotein
Antigen namehemagglutinin
Antigen speciesINFLUENZA A VIRUS (A/VIET NAM/1203/2004(H5N1))
Antigen sequenceGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR/ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

CDR Sequences (chothia definition)
CDRH1GGPFRSY
CDRH2IPIFGT
CDRH3HMGYQVRETMDV
CDRL1SGSSSNIGNDYVS
CDRL2DNNKRPS
CDRL3ATWDRRPTAYVV

Orientation Angles (from ABangle)
HL-56.06°
HC172.58°
HC2120.98°
LC1120.62°
LC286.37°
dc15.98Å
>   I/M
Fv Details
Heavy chainI
Light chainM
Heavy subgroupIGHV1
Light subgroupIGLV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 52A 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G A E V K K P G S S V K V S C K A S G G P F R S Y A I S W V R Q A P G Q G P E W M G G I I P I F G T T K Y A P K F Q G R V T I T A D D F A G T V Y M E L S S L R S E D T A M Y Y C A K H M G Y Q V R E T M D V W G K G T T V T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 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 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q P P S V S A A P G Q K V T I S C S G S S S N I G N D Y V S W Y Q Q L P G T A P K L L I Y D N N K R P S G I P D R F S G S K S G T S A T L G I T G L Q T G D E A N Y Y C A T W D R R P T A Y V V F G G G T K L T V L

Antigen Details
Antigen chainsD,C
Antigen typeprotein
Antigen namehemagglutinin
Antigen speciesINFLUENZA A VIRUS (A/VIET NAM/1203/2004(H5N1))
Antigen sequenceGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR/ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

CDR Sequences (chothia definition)
CDRH1GGPFRSY
CDRH2IPIFGT
CDRH3HMGYQVRETMDV
CDRL1SGSSSNIGNDYVS
CDRL2DNNKRPS
CDRL3ATWDRRPTAYVV

Orientation Angles (from ABangle)
HL-55.98°
HC172.87°
HC2120.45°
LC1118.79°
LC286.83°
dc16.18Å
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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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