Structure Viewer: 9b6w

>   Structure details

Envelope Protein asu of Yfv-Es504 with Yfv-17D Diii in complex with 2C9 Fab

PDB9b6w
SpeciesMUS MUSCULUS
MethodELECTRON MICROSCOPY
Resolution3.6Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 3 Fv(s).

>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV5
Light subgroupIGKV14
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112
E V K L V E S G G G L V K P G G S L K L S C A A S G F T F T N Y A M S W V R Q T P E K R L E W V A S I S S G H T P Y Y P D S V K G R F T I S R D N A R N I L F L Q M S S L R S E D T A M Y Y C A R G D Y Y G S V Y S A M D Y W G Q G T S L 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 99 100 101 102 103 104 105 106 107
E I R M T Q S P S S M Y A S L G E R V T V T C K A S Q D I N S Y L S W L Q Q K P G K S P K T L I Y R A N R L F D G V P S R F S G S G S G Q D Y S L T I S S L E Y E D M G I F Y C L Q Y D E F P F T F G S G T K L E L K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope protein
Antigen speciesYELLOW FEVER VIRUS
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDGPAEARKVCYSAVLTNVKINDKCPSTGEAHLEEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEAEFTGYGRATLECQVQTAVDFSNSYIAEMEKESWIVDKQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIKVLALGNQEGSLKTALTGAMRVTKDTNNSKLYKLHGGHVACRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHK

CDR Sequences (chothia definition)
CDRH1GFTFTNY
CDRH2SSGHT
CDRH3GDYYGSVYSAMDY
CDRL1KASQDINSYLS
CDRL2RANRLFD
CDRL3LQYDEFPFT

Orientation Angles (from ABangle)
HL-61.27°
HC171.73°
HC2119.28°
LC1119.32°
LC286.86°
dc16.01Å
>   F/G
Fv Details
Heavy chainF
Light chainG
Heavy subgroupIGHV5
Light subgroupIGKV14
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112
E V K L V E S G G G L V K P G G S L K L S C A A S G F T F T N Y A M S W V R Q T P E K R L E W V A S I S S G H T P Y Y P D S V K G R F T I S R D N A R N I L F L Q M S S L R S E D T A M Y Y C A R G D Y Y G S V Y S A M D Y W G Q G T S L 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 99 100 101 102 103 104 105 106 107
E I R M T Q S P S S M Y A S L G E R V T V T C K A S Q D I N S Y L S W L Q Q K P G K S P K T L I Y R A N R L F D G V P S R F S G S G S G Q D Y S L T I S S L E Y E D M G I F Y C L Q Y D E F P F T F G S G T K L E L K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nameenvelope protein
Antigen speciesYELLOW FEVER VIRUS
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDGPAEARKVCYSAVLTNVKINDKCPSTGEAHLEEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEAEFTGYGRATLECQVQTAVDFSNSYIAEMEKESWIVDKQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIKVLALGNQEGSLKTALTGAMRVTKDTNNSKLYKLHGGHVACRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHK

CDR Sequences (chothia definition)
CDRH1GFTFTNY
CDRH2SSGHT
CDRH3GDYYGSVYSAMDY
CDRL1KASQDINSYLS
CDRL2RANRLFD
CDRL3LQYDEFPFT

Orientation Angles (from ABangle)
HL-59.09°
HC171.47°
HC2118.72°
LC1120.4°
LC285.17°
dc15.74Å
>   H/I
Fv Details
Heavy chainH
Light chainI
Heavy subgroupIGHV5
Light subgroupIGKV14
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112
E V K L V E S G G G L V K P G G S L K L S C A A S G F T F T N Y A M S W V R Q T P E K R L E W V A S I S S G H T P Y Y P D S V K G R F T I S R D N A R N I L F L Q M S S L R S E D T A M Y Y C A R G D Y Y G S V Y S A M D Y W G Q G T S L 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 99 100 101 102 103 104 105 106 107
E I R M T Q S P S S M Y A S L G E R V T V T C K A S Q D I N S Y L S W L Q Q K P G K S P K T L I Y R A N R L F D G V P S R F S G S G S G Q D Y S L T I S S L E Y E D M G I F Y C L Q Y D E F P F T F G S G T K L E L K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope protein
Antigen speciesYELLOW FEVER VIRUS
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDGPAEARKVCYSAVLTNVKINDKCPSTGEAHLEEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEAEFTGYGRATLECQVQTAVDFSNSYIAEMEKESWIVDKQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIKVLALGNQEGSLKTALTGAMRVTKDTNNSKLYKLHGGHVACRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHK

CDR Sequences (chothia definition)
CDRH1GFTFTNY
CDRH2SSGHT
CDRH3GDYYGSVYSAMDY
CDRL1KASQDINSYLS
CDRL2RANRLFD
CDRL3LQYDEFPFT

Orientation Angles (from ABangle)
HL-62.13°
HC170.45°
HC2118.89°
LC1119.99°
LC284.72°
dc16.1Å
>   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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