Structure Viewer: 8tmy

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Crystal Structure of Sars-Cov-2 Spike Stem Helix Peptide in complex with Neutralizing antibody Chm-16

PDB8tmy
SpeciesMACACA MULATTA
MethodX-RAY DIFFRACTION
Resolution3.07Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E E Q L V E S G G G L V Q P G G S L R L S C T A S G F T L S T Y F M F W V R Q P P G K G L E W V S G I N L G G D K T W S T D S V K G R F T T S K E N A K N T L Y L Q M D S L R P E D T A V Y Y C A R L R S Q R G F D H W G Q G A 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 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 F T C R A S Q G V N N W L A W Y Q Q K P G K A P K L L I Y R A S N L E T G V P S R F S G S G S G T E F T L T I S S L Q P E D I A T Y Y C Q Q H D N F P Y T F G Q G T K V V I R

Antigen Details
Antigen chainsS
Antigen typepeptide
Antigen namestem helix peptide of spike protein s2'
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequencePLQPELDSFKEELDKYFKNHTSPDV

CDR Sequences (chothia definition)
CDRH1GFTLSTY
CDRH2NLGGDK
CDRH3LRSQRGFDH
CDRL1RASQGVNNWLA
CDRL2RASNLET
CDRL3QQHDNFPYT

Orientation Angles (from ABangle)
HL-53.1°
HC169.92°
HC2116.38°
LC1127.4°
LC289.28°
dc17.83Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E E Q L V E S G G G L V Q P G G S L R L S C T A S G F T L S T Y F M F W V R Q P P G K G L E W V S G I N L G G D K T W S T D S V K G R F T T S K E N A K N T L Y L Q M D S L R P E D T A V Y Y C A R L R S Q R G F D H W G Q G A 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 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 F T C R A S Q G V N N W L A W Y Q Q K P G K A P K L L I Y R A S N L E T G V P S R F S G S G S G T E F T L T I S S L Q P E D I A T Y Y C Q Q H D N F P Y T F G Q G T K V V I R

Antigen Details
Antigen chainsM
Antigen typepeptide
Antigen namestem helix peptide of spike protein s2'
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequencePLQPELDSFKEELDKYFKNHTSPDV

CDR Sequences (chothia definition)
CDRH1GFTLSTY
CDRH2NLGGDK
CDRH3LRSQRGFDH
CDRL1RASQGVNNWLA
CDRL2RASNLET
CDRL3QQHDNFPYT

Orientation Angles (from ABangle)
HL-54.99°
HC170.02°
HC2115.38°
LC1125.99°
LC288.24°
dc17.83Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E E Q L V E S G G G L V Q P G G S L R L S C T A S G F T L S T Y F M F W V R Q P P G K G L E W V S G I N L G G D K T W S T D S V K G R F T T S K E N A K N T L Y L Q M D S L R P E D T A V Y Y C A R L R S Q R G F D H W G Q G A 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 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 F T C R A S Q G V N N W L A W Y Q Q K P G K A P K L L I Y R A S N L E T G V P S R F S G S G S G T E F T L T I S S L Q P E D I A T Y Y C Q Q H D N F P Y T F G Q G T K V V I R

Antigen Details
Antigen chainsN
Antigen typepeptide
Antigen namestem helix peptide of spike protein s2'
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequencePLQPELDSFKEELDKYFKNHTSPDV

CDR Sequences (chothia definition)
CDRH1GFTLSTY
CDRH2NLGGDK
CDRH3LRSQRGFDH
CDRL1RASQGVNNWLA
CDRL2RASNLET
CDRL3QQHDNFPYT

Orientation Angles (from ABangle)
HL-54.36°
HC169.77°
HC2116.17°
LC1125.16°
LC288.34°
dc17.94Å
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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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