Structure Viewer: 8j1t

>   Structure details

Local Refined Cryo-Em Structure of Omicron Ba.5 Rbd in complex with 8-9D Fab

PDB8j1t
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.3Å
Number of Fvs1
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 1 Fv(s).

>   H/K
Fv Details
Heavy chainH
Light chainK
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

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

Light 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 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 96 97 98 99 100 101 102 103 104 105 106
D I Q M T Q S P S F L S A S V G D R V T I T C R A S Q G I S S Y L A W Y Q Q K P G K A P K L L I Y A A S T L Q S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q H L N S Y P S M Y T F G Q G T K V D I

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namespike protein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGP

CDR Sequences (chothia definition)
CDRH1GLTVSSN
CDRH2YPGGS
CDRH3DHSGHALDI
CDRL1RASQGISSYLA
CDRL2AASTLQS
CDRL3QHLNSYPSMYT

Orientation Angles (from ABangle)
HL-57.71°
HC174.91°
HC2114.56°
LC1119.66°
LC283.8°
dc16.48Å
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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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