Structure Viewer: 9c2h

>   Structure details

Sars-Cov-2 Nucleocapsid Dimerization Domain Bound to Fab-Np1E9 and Fab-Np3B4

PDB9c2h
SpeciesMUS SP.
MethodELECTRON MICROSCOPY
Resolution3.7Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionFalse
>   Structure visualisation
Please note the WebGL plugin needs to be enabled to use PV Viewer.

Display options:














>   Fv information

This PDB has 4 Fv(s).

>   B/C
Fv Details
Heavy chainB
Light chainC
Heavy subgroupIGHV6
Light subgroupIGKV4
SpeciesMUS SP.
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 52B 52C 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
E V Q L V E S G G G L V Q P G G S V K L S C L A S G F T F S D Y Y M S W V R Q S P E K G L E W V A E I R L E S D N Y A T H Y A E S V K G K F T I S R D D S K S R L Y L K M N S L R G E D T G I Y Y C A F D V Y Y G G A M D Y W G Q G T T V T V

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

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namenucleoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMAHHHHHHVDDDDKMENLYFQGMQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2RLESDNYA
CDRH3DVYYGGAMDY
CDRL1SASSSVSYMH
CDRL2DTSELAS
CDRL3FQGSGYPLT

Orientation Angles (from ABangle)
HL-55.42°
HC175.14°
HC2122.51°
LC1121.42°
LC281.34°
dc16.59Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV1
Light subgroupIGKV6
SpeciesMUS SP.
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 99 100 101 102 103 104 105 106 107 108 109 110 111
Q V Q L Q Q S G P E L V K P G T L V K I S C K A S G Y T F T S Y D I N W V K Q R P G Q G L E W I G W I Y P G D G S T K Y N E K F K G K A T L T A D T S S S T A Y M Q L N S L T S E N S A V Y F C A R G L V G A M D Y W G Q G T S V T V

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

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namenucleoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMAHHHHHHVDDDDKMENLYFQGMQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP

CDR Sequences (chothia definition)
CDRH1GYTFTSY
CDRH2YPGDGS
CDRH3GLVGAMDY
CDRL1KASQNVLNNVA
CDRL2SASYRYS
CDRL3QQYNSYPLT

Orientation Angles (from ABangle)
HL-59.52°
HC171.91°
HC2113.26°
LC1120.35°
LC283.05°
dc16.45Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV6
Light subgroupIGKV4
SpeciesMUS SP.
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 52B 52C 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
E V Q L V E S G G G L V Q P G G S V K L S C L A S G F T F S D Y Y M S W V R Q S P E K G L E W V A E I R L E S D N Y A T H Y A E S V K G K F T I S R D D S K S R L Y L K M N S L R G E D T G I Y Y C A F D V Y Y G G A M D Y W G Q G T T V T V

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

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namenucleoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMAHHHHHHVDDDDKMENLYFQGMQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2RLESDNYA
CDRH3DVYYGGAMDY
CDRL1SASSSVSYMH
CDRL2DTSELAS
CDRL3FQGSGYPLT

Orientation Angles (from ABangle)
HL-55.37°
HC174.49°
HC2122.07°
LC1120.85°
LC281.31°
dc16.61Å
>   I/J
Fv Details
Heavy chainI
Light chainJ
Heavy subgroupIGHV1
Light subgroupIGKV6
SpeciesMUS SP.
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 99 100 101 102 103 104 105 106 107 108 109 110 111
Q V Q L Q Q S G P E L V K P G T L V K I S C K A S G Y T F T S Y D I N W V K Q R P G Q G L E W I G W I Y P G D G S T K Y N E K F K G K A T L T A D T S S S T A Y M Q L N S L T S E N S A V Y F C A R G L V G A M D Y W G Q G T S V T V

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

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namenucleoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMAHHHHHHVDDDDKMENLYFQGMQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP

CDR Sequences (chothia definition)
CDRH1GYTFTSY
CDRH2YPGDGS
CDRH3GLVGAMDY
CDRL1KASQNVLNNVA
CDRL2SASYRYS
CDRL3QQYNSYPLT

Orientation Angles (from ABangle)
HL-59.78°
HC170.92°
HC2112.75°
LC1120.38°
LC282.76°
dc16.62Å
>   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]

Our privacy policy