Structure Viewer: 8dun

>   Structure details

Cryo-Em Structure of antibody Skw11 in complex with Western Equine Encephalitis Virus Spike (Local Refinement From Vlp Particles)

PDB8dun
SpeciesMACACA FASCICULARIS
MethodELECTRON MICROSCOPY
Resolution5.84Å
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 subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA FASCICULARIS
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C A V S G D S I S N N Y W T W I R H F P G K G L E W I G R I Y G D A G S T D Y N P S L K S R V T I S M D L S K N Q F S L D L T S V T V A D T A L Y Y C A S R T T V A D N W F D V W G P G V 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 T V T I T C R A T Q S I S S L L A W Y Q Y K P G K A P K L L I Y Q A S S L H I G V P S R F S G S G S G T D F T L T I S S L Q S E D F A T Y Y C Q Q H D S R P W T F G Q G T K V D I K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen namespike glycoprotein e2
Antigen speciesWESTERN EQUINE ENCEPHALITIS VIRUS
Antigen sequencePYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

CDR Sequences (chothia definition)
CDRH1GDSISNN
CDRH2YGDAGS
CDRH3RTTVADNWFDV
CDRL1RATQSISSLLA
CDRL2QASSLHI
CDRL3QQHDSRPWT

Orientation Angles (from ABangle)
HL-61.42°
HC177.01°
HC2120.16°
LC1121.46°
LC281.84°
dc16.7Å
>   I/M
Fv Details
Heavy chainI
Light chainM
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA FASCICULARIS
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C A V S G D S I S N N Y W T W I R H F P G K G L E W I G R I Y G D A G S T D Y N P S L K S R V T I S M D L S K N Q F S L D L T S V T V A D T A L Y Y C A S R T T V A D N W F D V W G P G V 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 T V T I T C R A T Q S I S S L L A W Y Q Y K P G K A P K L L I Y Q A S S L H I G V P S R F S G S G S G T D F T L T I S S L Q S E D F A T Y Y C Q Q H D S R P W T F G Q G T K V D I K

Antigen Details
Antigen chainsK
Antigen typeprotein
Antigen namespike glycoprotein e2
Antigen speciesWESTERN EQUINE ENCEPHALITIS VIRUS
Antigen sequencePYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

CDR Sequences (chothia definition)
CDRH1GDSISNN
CDRH2YGDAGS
CDRH3RTTVADNWFDV
CDRL1RATQSISSLLA
CDRL2QASSLHI
CDRL3QQHDSRPWT

Orientation Angles (from ABangle)
HL-61.42°
HC177.01°
HC2120.16°
LC1121.46°
LC281.84°
dc16.7Å
>   N/O
Fv Details
Heavy chainN
Light chainO
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA FASCICULARIS
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C A V S G D S I S N N Y W T W I R H F P G K G L E W I G R I Y G D A G S T D Y N P S L K S R V T I S M D L S K N Q F S L D L T S V T V A D T A L Y Y C A S R T T V A D N W F D V W G P G V 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 T V T I T C R A T Q S I S S L L A W Y Q Y K P G K A P K L L I Y Q A S S L H I G V P S R F S G S G S G T D F T L T I S S L Q S E D F A T Y Y C Q Q H D S R P W T F G Q G T K V D I K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namespike glycoprotein e2
Antigen speciesWESTERN EQUINE ENCEPHALITIS VIRUS
Antigen sequencePYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

CDR Sequences (chothia definition)
CDRH1GDSISNN
CDRH2YGDAGS
CDRH3RTTVADNWFDV
CDRL1RATQSISSLLA
CDRL2QASSLHI
CDRL3QQHDSRPWT

Orientation Angles (from ABangle)
HL-61.42°
HC177.01°
HC2120.16°
LC1121.46°
LC281.84°
dc16.7Å
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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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