Structure Viewer: 8hed

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Local Refinement of the Sars-Cov-2 Spike Trimer in complex with Rmab 9H1 Fab

PDB8hed
SpeciesORYCTOLAGUS CUNICULUS
MethodELECTRON MICROSCOPY
Resolution
Number of Fvs1
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 1 Fv(s).

>   G/F
Fv Details
Heavy chainG
Light chainF
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

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 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
S V E E S G G R L V T P G T P L T L T C T V S G F S L S R Y A M S W V R Q A P G K G L E W I G I I V D S G H T A Y A S W A K G R F T I S R T S T T V D L K M T S L T T E D T A T Y F C A R E T G G G A F Y V F E F W G P G T V V T V S S

Light 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 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 95C 95D 96 97 98 99 100 101 102 103 104 105 106 107
Q V L T Q T P S S V S A A V G G T V T I N C Q A S E D I Y D N L V W Y Q Q K P G Q P P K L L I Y D A S T L A F G V S S R F R G S G S G T H F T L T M R D V Q C D D A A T Y Y C Q G E F S C S S G D C T A F G G G T E V V V K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS

CDR Sequences (chothia definition)
CDRH1GFSLSRY
CDRH2VDSGH
CDRH3ETGGGAFYVFEF
CDRL1QASEDIYDNLV
CDRL2DASTLAF
CDRL3QGEFSCSSGDCTA

Orientation Angles (from ABangle)
HL-55.56°
HC171.9°
HC2120.13°
LC1120.37°
LC281.58°
dc17.01Å
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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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