Structure Viewer: 7wp8

>   Structure details

Cryo-Em Structure of Sars-Cov-2 Recombinant Spike Protein Stfk1628X in complex with Three Neutralizing antibodies

PDB7wp8
SpeciesMUS MUSCULUS
MethodELECTRON MICROSCOPY
Resolution3.88Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 3 Fv(s).

>   D/C
Fv Details
Heavy chainD
Light chainC
Heavy subgroupIGHV1
Light subgroupIGKV6
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q L A Q S G A E L A R P G A S V K L S C K A S G Y T F T R Y W M Q W V K Q R P G Q G L E W I G A I Y P G D G D S R Y T Q K F K G K A T L T A D K S S S T A Y M Q L S S L A S E D S A V Y Y C A R R N Y Y G Y D A F A Y W G Q G T L V T V S A

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

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGTIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELL

CDR Sequences (chothia definition)
CDRH1GYTFTRY
CDRH2YPGDGD
CDRH3RNYYGYDAFAY
CDRL1KASQDVDTAVA
CDRL2WASTRHT
CDRL3QQYSPYPYT

Orientation Angles (from ABangle)
HL-56.09°
HC172.87°
HC2111.66°
LC1119.81°
LC279.64°
dc16.2Å
>   E/G
Fv Details
Heavy chainE
Light chainG
Heavy subgroupIGHV1
Light subgroupIGKV8
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 V Q L Q Q P G A E L V R P G A S V K L S C K A S G Y T F T S Y W M N W V K Q R P E Q G L E W I G R I D P Y D S E T H Y N Q K F K D K A I L T V D K S S T T A Y M Q L S S L T S E D S A V Y Y C A R W G T V E W F F D Y W G Q G T T L T V S Q

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 30A 30B 30C 30D 30E 30F 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 M T Q S P S S L A M S V G Q K V T M S C K S S Q S L L N S Y N Q E N Y L A W Y Q Q K P G Q S P K L L V Y F A S T R E S G V P D R F I G S G S G T D F T L T I S S V Q A E D L A D Y F C Q Q H Y S T P F T F G S G T K L E I K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGTIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELL

CDR Sequences (chothia definition)
CDRH1GYTFTSY
CDRH2DPYDSE
CDRH3WGTVEWFFDY
CDRL1KSSQSLLNSYNQENYLA
CDRL2FASTRES
CDRL3QQHYSTPFT

Orientation Angles (from ABangle)
HL-61.22°
HC172.67°
HC2113.56°
LC1119.58°
LC280.82°
dc16.01Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q S G P E L V K P G A S V R I S C K A S G Y T F T S Y Y I H W V K Q R P G Q G L E W I G W I Y P G N V K S I Y N E K F K G K A T L T A D K S S N T A Y M Q L S S L T S E D S A V Y F C A G E E H G N Y F D F W G Q G T T L T V S Q

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 94 95 96 97 98 99 100 101 102 103 104 105 106 107
Q I V L S Q S P T I L S A S P G E K V T M T C R A N S S V G F M H W C Q Q K P G S S P K P W I Y A T S N L A S G V P G R F S G S G S G T S Y S L T I S R V E A E D A A T Y Y C Q Q W S S D P P T F G S G T K L E I K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGTIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELL

CDR Sequences (chothia definition)
CDRH1GYTFTSY
CDRH2YPGNVK
CDRH3EEHGNYFDF
CDRL1RANSSVGFMH
CDRL2ATSNLAS
CDRL3QQWSSDPPT

Orientation Angles (from ABangle)
HL-53.63°
HC171.22°
HC2113.54°
LC1123.48°
LC280.58°
dc16.99Å
>   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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