Structure Viewer: 7np1

>   Structure details

Crystal Structure of the Sars-Cov-2 Receptor Binding Domain in complex with antibody Ion-360

PDB7np1
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.8Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   I/M
Fv Details
Heavy chainI
Light chainM
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 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V Q S G G G L V K P G G S L R L S C A A S G I T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T 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 R G E G G S I V G V T S 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R 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 E T E F T L T I S S L H P D D F A T Y Y C Q Q S Y S T L P Y T F G Q G T K V E I K

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

CDR Sequences (chothia definition)
CDRH1GITVSSN
CDRH2YSGGS
CDRH3GEGGSIVGVTSDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTLPYT

Orientation Angles (from ABangle)
HL-62.22°
HC173.21°
HC2117.82°
LC1123.04°
LC286.66°
dc16.25Å
>   K/O
Fv Details
Heavy chainK
Light chainO
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 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V Q S G G G L V K P G G S L R L S C A A S G I T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T 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 R G E G G S I V G V T S 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R 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 E T E F T L T I S S L H P D D F A T Y Y C Q Q S Y S T L P Y T F G Q G T K V E I K

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLPATVCGPKKSTNLVKNKCVNFAAAGSHHHHHH

CDR Sequences (chothia definition)
CDRH1GITVSSN
CDRH2YSGGS
CDRH3GEGGSIVGVTSDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTLPYT

Orientation Angles (from ABangle)
HL-65.72°
HC174.94°
HC2116.34°
LC1119.46°
LC287.83°
dc16.52Å
>   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 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V Q S G G G L V K P G G S L R L S C A A S G I T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T 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 R G E G G S I V G V T S 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R 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 E T E F T L T I S S L H P D D F A T Y Y C Q Q S Y S T L P Y T F G Q G T K V E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLPATVCGPKKSTNLVKNKCVNFAAAGSHHHHHH

CDR Sequences (chothia definition)
CDRH1GITVSSN
CDRH2YSGGS
CDRH3GEGGSIVGVTSDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTLPYT

Orientation Angles (from ABangle)
HL-62.06°
HC173.26°
HC2118.13°
LC1123.35°
LC286.1°
dc16.11Å
>   J/N
Fv Details
Heavy chainJ
Light chainN
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 100B 100C 100D 100E 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V Q S G G G L V K P G G S L R L S C A A S G I T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T 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 R G E G G S I V G V T S 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R 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 E T E F T L T I S S L H P D D F A T Y Y C Q Q S Y S T L P Y T F G Q G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLPATVCGPKKSTNLVKNKCVNFAAAGSHHHHHH

CDR Sequences (chothia definition)
CDRH1GITVSSN
CDRH2YSGGS
CDRH3GEGGSIVGVTSDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTLPYT

Orientation Angles (from ABangle)
HL-64.23°
HC174.59°
HC2117.73°
LC1121.74°
LC287.89°
dc16.39Å
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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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