Structure Viewer: 8dww

>   Structure details

Chikungunya Vlp in complex with Neutralizing Fab 506.a08 (asymmetric Unit)

PDB8dww
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.13Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 4 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112
E E Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S S Y S M N W V R Q A P G K G L E W V S Y I S S S S S T I H Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R E G N S G Y E P L D Y W G Q G T L V T V 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P W T F G Q G T K V E I

Antigen Details
Antigen chainsN
Antigen typeprotein
Antigen namee2 glycoprotein
Antigen speciesCHIKUNGUNYA VIRUS STRAIN SENEGAL 37997
Antigen sequenceNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2SSSSST
CDRH3EGNSGYEPLDY
CDRL1RASQSISSYLN
CDRL2AASSLQS
CDRL3QQSYSTPWT

Orientation Angles (from ABangle)
HL-55.99°
HC172.54°
HC2115.02°
LC1116.89°
LC284.5°
dc17.77Å
>   V/U
Fv Details
Heavy chainV
Light chainU
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112
E E Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S S Y S M N W V R Q A P G K G L E W V S Y I S S S S S T I H Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R E G N S G Y E P L D Y W G Q G T L V T V 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P W T F G Q G T K V E I

Antigen Details
Antigen chainsM
Antigen typeprotein
Antigen namee2 glycoprotein
Antigen speciesCHIKUNGUNYA VIRUS STRAIN SENEGAL 37997
Antigen sequenceNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2SSSSST
CDRH3EGNSGYEPLDY
CDRL1RASQSISSYLN
CDRL2AASSLQS
CDRL3QQSYSTPWT

Orientation Angles (from ABangle)
HL-55.99°
HC170.39°
HC2115.35°
LC1117.91°
LC282.18°
dc18.19Å
>   X/W
Fv Details
Heavy chainX
Light chainW
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112
E E Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S S Y S M N W V R Q A P G K G L E W V S Y I S S S S S T I H Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R E G N S G Y E P L D Y W G Q G T L V T V 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P W T F G Q G T K V E I

Antigen Details
Antigen chainsO
Antigen typeprotein
Antigen namee2 glycoprotein
Antigen speciesCHIKUNGUNYA VIRUS STRAIN SENEGAL 37997
Antigen sequenceNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2SSSSST
CDRH3EGNSGYEPLDY
CDRL1RASQSISSYLN
CDRL2AASSLQS
CDRL3QQSYSTPWT

Orientation Angles (from ABangle)
HL-56.12°
HC170.44°
HC2114.48°
LC1118.55°
LC284.17°
dc17.84Å
>   Z/Y
Fv Details
Heavy chainZ
Light chainY
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112
E E Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S S Y S M N W V R Q A P G K G L E W V S Y I S S S S S T I H Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R E G N S G Y E P L D Y W G Q G T L V T V 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
D I Q M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P W T F G Q G T K V E I

Antigen Details
Antigen chainsP
Antigen typeprotein
Antigen namee2 glycoprotein
Antigen speciesCHIKUNGUNYA VIRUS STRAIN SENEGAL 37997
Antigen sequenceNFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2SSSSST
CDRH3EGNSGYEPLDY
CDRL1RASQSISSYLN
CDRL2AASSLQS
CDRL3QQSYSTPWT

Orientation Angles (from ABangle)
HL-55.94°
HC172.1°
HC2116.01°
LC1118.44°
LC282.47°
dc17.59Å
>   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]

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