Structure Viewer: 6dfg

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Bg505 Md39 Sosip Trimer in complex with Mature Bg18 Fragment antigen Binding

PDB6dfg
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution4.42Å
Number of Fvs3
In complexTrue
Light chain typeLambda
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupunknown
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 31A 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 100F 100G 100H 100I 100J 100K 100L 100M 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L R E S G P G L V K P S E T L S L S C T V S N D S R P S D H S W T W V R Q S P G K A L E W I G D I H Y N G A T T Y N P S L R S R V R I E L D Q S I P R F S L K M T S M T A A D T G M Y Y C A R N A I R I Y G V V A L G E W F H Y G M D V W G Q G T A 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 96 97 98 99 100 101 102 103 104 105 106 107
S S E L T Q P P S V S V S P G Q T A R I T C S G A P L T S R F T Y W Y R Q K P G Q A P V L I I S R S S Q R S S G W S G R F S A S W S G T T V T L T I R G V Q A D D E A D Y Y C Q S S D T S D S Y K M F G G G T K L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGR

CDR Sequences (chothia definition)
CDRH1NDSRPSDH
CDRH2HYNGA
CDRH3NAIRIYGVVALGEWFHYGMDV
CDRL1SGAPLTSRFTY
CDRL2RSSQRSS
CDRL3QSSDTSDSYKM

Orientation Angles (from ABangle)
HL-55.58°
HC173.2°
HC2121.96°
LC1120.64°
LC286.06°
dc16.62Å
>   G/J
Fv Details
Heavy chainG
Light chainJ
Heavy subgroupunknown
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 31A 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 100F 100G 100H 100I 100J 100K 100L 100M 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L R E S G P G L V K P S E T L S L S C T V S N D S R P S D H S W T W V R Q S P G K A L E W I G D I H Y N G A T T Y N P S L R S R V R I E L D Q S I P R F S L K M T S M T A A D T G M Y Y C A R N A I R I Y G V V A L G E W F H Y G M D V W G Q G T A 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 96 97 98 99 100 101 102 103 104 105 106 107
S S E L T Q P P S V S V S P G Q T A R I T C S G A P L T S R F T Y W Y R Q K P G Q A P V L I I S R S S Q R S S G W S G R F S A S W S G T T V T L T I R G V Q A D D E A D Y Y C Q S S D T S D S Y K M F G G G T K L T V L

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGR

CDR Sequences (chothia definition)
CDRH1NDSRPSDH
CDRH2HYNGA
CDRH3NAIRIYGVVALGEWFHYGMDV
CDRL1SGAPLTSRFTY
CDRL2RSSQRSS
CDRL3QSSDTSDSYKM

Orientation Angles (from ABangle)
HL-54.08°
HC173.0°
HC2119.97°
LC1119.68°
LC286.29°
dc16.58Å
>   I/K
Fv Details
Heavy chainI
Light chainK
Heavy subgroupunknown
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 31A 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 100F 100G 100H 100I 100J 100K 100L 100M 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L R E S G P G L V K P S E T L S L S C T V S N D S R P S D H S W T W V R Q S P G K A L E W I G D I H Y N G A T T Y N P S L R S R V R I E L D Q S I P R F S L K M T S M T A A D T G M Y Y C A R N A I R I Y G V V A L G E W F H Y G M D V W G Q G T A 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 96 97 98 99 100 101 102 103 104 105 106 107
S S E L T Q P P S V S V S P G Q T A R I T C S G A P L T S R F T Y W Y R Q K P G Q A P V L I I S R S S Q R S S G W S G R F S A S W S G T T V T L T I R G V Q A D D E A D Y Y C Q S S D T S D S Y K M F G G G T K L T V L

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGR

CDR Sequences (chothia definition)
CDRH1NDSRPSDH
CDRH2HYNGA
CDRH3NAIRIYGVVALGEWFHYGMDV
CDRL1SGAPLTSRFTY
CDRL2RSSQRSS
CDRL3QSSDTSDSYKM

Orientation Angles (from ABangle)
HL-54.4°
HC172.75°
HC2121.29°
LC1120.49°
LC285.65°
dc16.93Å
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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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