Structure Viewer: 7pry

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Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in complex with Covox-45 and Beta-6 Fabs

PDB7pry
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.1Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV4
Light subgroupIGKV3
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 31A 31B 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 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G P G L V K P S E T L S L T C T V S G G S I S S S S H Y W G W I R Q P P G K G L E W I G S I Y Y S E S A Y Y N P S L K S R V T M S I D T S K N Q F S L K L N S V T A A D T A V Y Y C A R V T E P R W T S C Y F D Y W G Q G T L 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 95A 96 97 98 99 100 101 102 103 104 105 106 107
E I V M T Q S P A T L S L S P G E R A T L S C R T S Q S V T S Y L A W Y Q Q R P G Q A P R L L I Y D A S D R A T G I P A R F S G S G S G T D F T L T I S N L E P E D F A V Y Y C Q L R S N W P P I T F G Q G T R L E T K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen namesurface glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GGSISSSSH
CDRH2YYSES
CDRH3VTEPRWTSCYFDY
CDRL1RTSQSVTSYLA
CDRL2DASDRAT
CDRL3QLRSNWPPIT

Orientation Angles (from ABangle)
HL-58.81°
HC172.16°
HC2121.9°
LC1121.76°
LC284.94°
dc16.27Å
>   A/B
Fv Details
Heavy chainA
Light chainB
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 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
Q V Q L V E S G G G V V Q P G R S L R L S C A A S G F T F S T Y A M H W V R Q A P G K G L E W V A V L S Y D G S N K Y Y A D S V K 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 K G G S Y A Y Y Y Y M D V W G K 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 S L S A S V G D R V T I T C Q A S Q D I S N Y L N W Y Q Q K P G K A P K L L I Y D A S N L E T G V P S R F S G G G S G T D F T F T I T S L Q P E D I A T Y Y C Q Q Y D N L P L T F G G G T K V D I K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen namesurface glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTFSTY
CDRH2SYDGSN
CDRH3GGSYAYYYYMDV
CDRL1QASQDISNYLN
CDRL2DASNLET
CDRL3QQYDNLPLT

Orientation Angles (from ABangle)
HL-49.52°
HC178.01°
HC2119.8°
LC1118.34°
LC288.05°
dc16.4Å
>   F/G
Fv Details
Heavy chainF
Light chainG
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 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
Q V Q L V E S G G G V V Q P G R S L R L S C A A S G F T F S T Y A M H W V R Q A P G K G L E W V A V L S Y D G S N K Y Y A D S V K 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 K G G S Y A Y Y Y Y M D V W G K 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 S L S A S V G D R V T I T C Q A S Q D I S N Y L N W Y Q Q K P G K A P K L L I Y D A S N L E T G V P S R F S G G G S G T D F T F T I T S L Q P E D I A T Y Y C Q Q Y D N L P L T F G G G T K V D I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namesurface glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTFSTY
CDRH2SYDGSN
CDRH3GGSYAYYYYMDV
CDRL1QASQDISNYLN
CDRL2DASNLET
CDRL3QQYDNLPLT

Orientation Angles (from ABangle)
HL-47.91°
HC178.44°
HC2120.1°
LC1118.21°
LC288.86°
dc16.36Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV3
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 31A 31B 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 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G P G L V K P S E T L S L T C T V S G G S I S S S S H Y W G W I R Q P P G K G L E W I G S I Y Y S E S A Y Y N P S L K S R V T M S I D T S K N Q F S L K L N S V T A A D T A V Y Y C A R V T E P R W T S C Y F D Y W G Q G T L 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 95A 96 97 98 99 100 101 102 103 104 105 106 107
E I V M T Q S P A T L S L S P G E R A T L S C R T S Q S V T S Y L A W Y Q Q R P G Q A P R L L I Y D A S D R A T G I P A R F S G S G S G T D F T L T I S N L E P E D F A V Y Y C Q L R S N W P P I T F G Q G T R L E T K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namesurface glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GGSISSSSH
CDRH2YYSES
CDRH3VTEPRWTSCYFDY
CDRL1RTSQSVTSYLA
CDRL2DASDRAT
CDRL3QLRSNWPPIT

Orientation Angles (from ABangle)
HL-58.89°
HC172.06°
HC2121.74°
LC1121.54°
LC284.88°
dc16.24Å
>   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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