Structure Viewer: 8def

>   Structure details

Cryo-Em Structure of Western Equine Encephalitis Virus Vlp in complex with Skw24 Fab

PDB8def
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution4.2Å
Number of Fvs2
In complexTrue
Light chain typeLambda
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   S/T
Fv Details
Heavy chainS
Light chainT
Heavy subgroupIGHV3
Light subgroupIGLV3
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 52B 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C V A S G F T F S D Y R M A W V R Q A T G K G L E W V S T I S Q P S G T N T Y Y L D P V K G R F T V S R D N A K N T L Y L Q M H S L R A E D T A V Y Y C A R V V T E S R P P A A 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 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S Y E L T Q P P S V S A S P G Q T A R I T C G G I N I G S E L V H W Y Q Q K P P Q A P V L V I Y A N G E R P S G I P E R F S G S N S G N T A T L T I S G V E A G D E A D Y Y C Q L W D I S S D H N Y I F G D G T R L T V L

Antigen Details
Antigen chainsG,F
Antigen typeprotein
Antigen namespike glycoprotein e2; spike glycoprotein e1
Antigen speciesWESTERN EQUINE ENCEPHALITIS VIRUS
Antigen sequenceSITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI/FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCRFHTVIPSPQVKCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAVALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIRKGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGYEMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVSCTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSSPQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSLIVVGLIVLVCSSMLINTRR

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2SQPSGTN
CDRH3VVTESRPPAAWFDV
CDRL1GGINIGSELVH
CDRL2ANGERPS
CDRL3QLWDISSDHNYI

Orientation Angles (from ABangle)
HL-58.01°
HC175.57°
HC2121.57°
LC1117.81°
LC287.78°
dc16.82Å
>   U/V
Fv Details
Heavy chainU
Light chainV
Heavy subgroupIGHV3
Light subgroupIGLV3
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 52B 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C V A S G F T F S D Y R M A W V R Q A T G K G L E W V S T I S Q P S G T N T Y Y L D P V K G R F T V S R D N A K N T L Y L Q M H S L R A E D T A V Y Y C A R V V T E S R P P A A 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 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S Y E L T Q P P S V S A S P G Q T A R I T C G G I N I G S E L V H W Y Q Q K P P Q A P V L V I Y A N G E R P S G I P E R F S G S N S G N T A T L T I S G V E A G D E A D Y Y C Q L W D I S S D H N Y I F G D G T R L T V L

Antigen Details
Antigen chainsK,J
Antigen typeprotein
Antigen namespike glycoprotein e2; spike glycoprotein e1
Antigen speciesWESTERN EQUINE ENCEPHALITIS VIRUS
Antigen sequenceSITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI/FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCRFHTVIPSPQVKCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAVALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIRKGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGYEMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVSCTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSSPQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSLIVVGLIVLVCSSMLINTRR

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2SQPSGTN
CDRH3VVTESRPPAAWFDV
CDRL1GGINIGSELVH
CDRL2ANGERPS
CDRL3QLWDISSDHNYI

Orientation Angles (from ABangle)
HL-59.91°
HC174.85°
HC2121.34°
LC1118.87°
LC286.22°
dc16.83Å
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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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