Structure Viewer: 8iv8

>   Structure details

Cryo-Em Structure of Sars-Cov-2 Spike Protein in complex with Double Nabs 3E2 and 1C4 (Local Refinement)

PDB8iv8
SpeciesMUS MUSCULUS
MethodELECTRON MICROSCOPY
Resolution3.92Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 2 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV5
Light subgroupIGKV4
SpeciesMUS MUSCULUS
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 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 M L V E S G G G V V K P G G S L K L S C A A S G F S F S T Y A M S W I R Q T P E K S L E W V A A I S S G G T N T Y Y P G S V K G R F T I S R D K A M N T L Y L Q L S S L R S E D T A M Y Y C V R H S G N Y V D S V M D Y W G Q G T S 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 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 96 97 98 99 100 101 102 103 104 105 106 107
Q I V L T Q S P A I M S A S L G E E I T L T C S V S S S V S D M H W Y Q Q K S G T S P K V F I Y S T S N L A S G V P S R F S G S G S G T F Y S L T I S S V E A E D A A Y Y Y C H Q W S S W T F G G G T K L E I K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP

CDR Sequences (chothia definition)
CDRH1GFSFSTY
CDRH2SSGGTN
CDRH3HSGNYVDSVMDY
CDRL1SVSSSVSDMH
CDRL2STSNLAS
CDRL3HQWSSWT

Orientation Angles (from ABangle)
HL-59.09°
HC172.67°
HC2118.58°
LC1116.81°
LC283.23°
dc16.54Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV9
Light subgroupIGKV5
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q I Q L V Q S G P E L K K P G E T V K I S C K A S G Y T F T D Y G L N W V K Q A P G K G L K W M G W I N T Y S G E P T Y N D E F R G R F A F S L E T S T I T A Y L K I N N L K N E D T A T Y F C A R G G N W D W Y F D V W G A 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 V L T Q S P A T L S V T P G D N V S L S C R A S Q I I S N N L H W Y Q Q K S H E S P R L L I K Y A S Q S I S G I P S R F S G S G S G T D F T L S I N S V E T E D F G M Y F C Q Q S N T W P L T C G S G T K L E L N

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP

CDR Sequences (chothia definition)
CDRH1GYTFTDY
CDRH2NTYSGE
CDRH3GGNWDWYFDV
CDRL1RASQIISNNLH
CDRL2YASQSIS
CDRL3QQSNTWPLT

Orientation Angles (from ABangle)
HL-58.32°
HC174.16°
HC2113.35°
LC1121.67°
LC283.24°
dc16.69Å
>   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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