Structure Viewer: 8hwt

>   Structure details

Sars-Cov-2 Omicron Ba.2 Rbd complexed with Bd-604 and S304 Fab

PDB8hwt
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution2.91Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L I Q P G G S L R L S C A A S G I I V S S N Y M T W V R Q A P G K G L E W V S V I Y S G G S T F Y A D S V K G R F T I S R D N S K N T L Y L Q M S S L R A E D T A V Y Y C A R D L G P Y G M D V W G Q G T T V T V S 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q L 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 D L A W Y Q Q K P G K A P N 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 Q L N S D L Y T F G Q G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namespike protein s2'
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

CDR Sequences (chothia definition)
CDRH1GIIVSSN
CDRH2YSGGS
CDRH3DLGPYGMDV
CDRL1RASQGISSDLA
CDRL2AASTLQS
CDRL3QQLNSDLYT

Orientation Angles (from ABangle)
HL-60.15°
HC172.11°
HC2118.28°
LC1120.83°
LC283.0°
dc16.94Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 100B 100C 100D 101 102 103 104 105 106 107 108 109 110 111 112 113
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 S Y D M H W V R Q T T G K G L E W V S T I G T A G D T Y Y P D S V K G R F T I S R E D A K N S L Y L Q M N S L R A G D T A V Y Y C A R G D S S G Y Y Y Y F D Y W G Q G T L L T V S 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 96 97 98 99 100 101 102 103 104 105 106 107
D I E M T Q S P S S L S A A V G D R V T I T C R A S Q S I G S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A I Y Y C Q Q S Y V S P T Y T F G P G T K V D I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namespike protein s2'
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2GTAGD
CDRH3GDSSGYYYYFDY
CDRL1RASQSIGSYLN
CDRL2AASSLQS
CDRL3QQSYVSPTYT

Orientation Angles (from ABangle)
HL-65.76°
HC173.83°
HC2116.3°
LC1119.09°
LC283.82°
dc16.75Å
>   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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