Structure Viewer: 7pqz

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Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in complex with Fi-3a and Fd-11a Fabs

PDB7pqz
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.2Å
Number of Fvs2
In complexTrue
Light chain typeKappa,Lambda
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 L E S G G G L I Q P G G S L R L S C A A S G F 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 D H V R P G M N I W G Q G T M 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
A I R M 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 S G S G T D F T F T I S S L Q P E D I A T Y Y C Q Q Y D N L P V T F G G G T K V D I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTVSSN
CDRH2YSGGS
CDRH3DHVRPGMNI
CDRL1QASQDISNYLN
CDRL2DASNLET
CDRL3QQYDNLPVT

Orientation Angles (from ABangle)
HL-58.43°
HC172.82°
HC2118.42°
LC1119.03°
LC283.38°
dc16.35Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGLV1
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 100E 100F 100G 100H 100I 100J 101 102 103 104 105 106 107 108 109 110 111 112 113
E 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 S Y G M H W V R Q A P G K G L E W V A V I W 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 P D I L T G Y Y N Y Y Y Y G M D V W G Q G T M V T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 30C 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 95B 95C 95D 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q P P S V S G A P G Q R V T I S C T G S S S N I G A G Y D V H W Y Q Q L P G T A P K L L I Y G N S N R P S G V P D R F S G S K S G T S A S L A I T G L Q A E D E A D Y Y C Q S Y D S S L S G F Y V V F G G G T K L T V L

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2WYDGSN
CDRH3GPDILTGYYNYYYYGMDV
CDRL1TGSSSNIGAGYDVH
CDRL2GNSNRPS
CDRL3QSYDSSLSGFYVV

Orientation Angles (from ABangle)
HL-56.17°
HC171.44°
HC2119.39°
LC1118.51°
LC282.7°
dc15.91Å
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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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