Structure Viewer: 3csy

>   Structure details

Crystal Structure of the Trimeric Prefusion Ebola Virus Glycoprotein in complex with a Neutralizing antibody From a Human Survivor

PDB3csy
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.4Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
>   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).

>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV3
Light subgroupIGKV4
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V K P G G S L R L S C A A S G F T L I N Y R M N W V R Q A P G K G L E W V S S I S S S S S Y I H Y A D S V K G R F T I S R D N A E N S L Y L Q M N S L R A E D T A V Y Y C V R E G P R A T G Y S M A D V F D 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 30A 30B 30C 30D 30E 30F 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
E L V M T Q S P D S L A V S L G E R A T I N C K S S Q S V L Y S S N N K S Y L A W Y Q Q K P G Q P P K L L I Y W A S T R E S G V P D R F S G S G S G T D F T L T I S S L Q A E D V A V Y Y C Q Q Y Y S A P L T F G G G T K V E I K

Antigen Details
Antigen chainsL,K
Antigen typeprotein
Antigen nameenvelope glycoprotein gp2; envelope glycoprotein gp1
Antigen speciesZAIRE EBOLA VIRUS
Antigen sequenceEAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD/YPYDVPDYAIEGRGARSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNEVEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

CDR Sequences (chothia definition)
CDRH1GFTLINY
CDRH2SSSSSY
CDRH3EGPRATGYSMADVFDI
CDRL1KSSQSVLYSSNNKSYLA
CDRL2WASTRES
CDRL3QQYYSAPLT

Orientation Angles (from ABangle)
HL-62.82°
HC171.24°
HC2117.11°
LC1118.82°
LC282.46°
dc16.48Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV3
Light subgroupIGKV4
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V K P G G S L R L S C A A S G F T L I N Y R M N W V R Q A P G K G L E W V S S I S S S S S Y I H Y A D S V K G R F T I S R D N A E N S L Y L Q M N S L R A E D T A V Y Y C V R E G P R A T G Y S M A D V F D 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 30A 30B 30C 30D 30E 30F 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
E L V M T Q S P D S L A V S L G E R A T I N C K S S Q S V L Y S S N N K S Y L A W Y Q Q K P G Q P P K L L I Y W A S T R E S G V P D R F S G S G S G T D F T L T I S S L Q A E D V A V Y Y C Q Q Y Y S A P L T F G G G T K V E I K

Antigen Details
Antigen chainsP,O
Antigen typeprotein
Antigen nameenvelope glycoprotein gp2; envelope glycoprotein gp1
Antigen speciesZAIRE EBOLA VIRUS
Antigen sequenceEAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD/YPYDVPDYAIEGRGARSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNEVEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

CDR Sequences (chothia definition)
CDRH1GFTLINY
CDRH2SSSSSY
CDRH3EGPRATGYSMADVFDI
CDRL1KSSQSVLYSSNNKSYLA
CDRL2WASTRES
CDRL3QQYYSAPLT

Orientation Angles (from ABangle)
HL-62.14°
HC172.07°
HC2117.69°
LC1119.71°
LC283.33°
dc16.4Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV4
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V K P G G S L R L S C A A S G F T L I N Y R M N W V R Q A P G K G L E W V S S I S S S S S Y I H Y A D S V K G R F T I S R D N A E N S L Y L Q M N S L R A E D T A V Y Y C V R E G P R A T G Y S M A D V F D 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 30A 30B 30C 30D 30E 30F 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
E L V M T Q S P D S L A V S L G E R A T I N C K S S Q S V L Y S S N N K S Y L A W Y Q Q K P G Q P P K L L I Y W A S T R E S G V P D R F S G S G S G T D F T L T I S S L Q A E D V A V Y Y C Q Q Y Y S A P L T F G G G T K V E I K

Antigen Details
Antigen chainsN,M
Antigen typeprotein
Antigen nameenvelope glycoprotein gp2; envelope glycoprotein gp1
Antigen speciesZAIRE EBOLA VIRUS
Antigen sequenceEAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD/YPYDVPDYAIEGRGARSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNEVEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

CDR Sequences (chothia definition)
CDRH1GFTLINY
CDRH2SSSSSY
CDRH3EGPRATGYSMADVFDI
CDRL1KSSQSVLYSSNNKSYLA
CDRL2WASTRES
CDRL3QQYYSAPLT

Orientation Angles (from ABangle)
HL-62.63°
HC171.62°
HC2117.3°
LC1118.59°
LC282.79°
dc16.46Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV4
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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V K P G G S L R L S C A A S G F T L I N Y R M N W V R Q A P G K G L E W V S S I S S S S S Y I H Y A D S V K G R F T I S R D N A E N S L Y L Q M N S L R A E D T A V Y Y C V R E G P R A T G Y S M A D V F D 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 30A 30B 30C 30D 30E 30F 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
E L V M T Q S P D S L A V S L G E R A T I N C K S S Q S V L Y S S N N K S Y L A W Y Q Q K P G Q P P K L L I Y W A S T R E S G V P D R F S G S G S G T D F T L T I S S L Q A E D V A V Y Y C Q Q Y Y S A P L T F G G G T K V E I K

Antigen Details
Antigen chainsJ,I
Antigen typeprotein
Antigen nameenvelope glycoprotein gp2; envelope glycoprotein gp1
Antigen speciesZAIRE EBOLA VIRUS
Antigen sequenceEAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVD/YPYDVPDYAIEGRGARSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNEVEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

CDR Sequences (chothia definition)
CDRH1GFTLINY
CDRH2SSSSSY
CDRH3EGPRATGYSMADVFDI
CDRL1KSSQSVLYSSNNKSYLA
CDRL2WASTRES
CDRL3QQYYSAPLT

Orientation Angles (from ABangle)
HL-63.88°
HC171.57°
HC2117.39°
LC1118.71°
LC282.35°
dc16.5Å
>   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