Structure Viewer: 7ll1

>   Structure details

Cryo-Em Structure of Bg505 Ds-Sosip in complex with Glycan276-Dependent Broadly Neutralizing antibody Vrc40.01 Fab

PDB7ll1
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.73Å
Number of Fvs3
In complexTrue
Light chain typeunknown
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 subgroupunknown
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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 70A 70B 70C 70D 70E 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L I Q S G P Q F K T P G A S V T V S C K A S G Y I F T D Y L I H W V R L V P G K G L E W L G R I N T N A G L M Y L S H K F E G R L I L R R V V D W R T P S L G T V N M E L R N V R S D D S A I Y F C G R V V D G F N A A G P L E F W G Q G S P V I 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
Q V V M T Q S P A T L S L S P G E T A A V S C R A S Q Y V D R S I S W Y Q L K T G R A P R L L V Y A A S S R S I G V P D R F S G S G S G R D F T L T I R G V Q S D D F A L Y Y C Q Q D Y Y W P V T F G Q G T R L D M K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

CDR Sequences (chothia definition)
CDRH1GYIFTDY
CDRH2NTNAGL
CDRH3VVDGFNAAGPLEF
CDRL1RASQYVDRSIS
CDRL2AASSRSI
CDRL3QQDYYWPVT

Orientation Angles (from ABangle)
HL-59.75°
HC173.77°
HC2115.04°
LC1119.72°
LC288.13°
dc15.94Å
>   J/K
Fv Details
Heavy chainJ
Light chainK
Heavy subgroupunknown
Light subgroupunknown
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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 70A 70B 70C 70D 70E 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L I Q S G P Q F K T P G A S V T V S C K A S G Y I F T D Y L I H W V R L V P G K G L E W L G R I N T N A G L M Y L S H K F E G R L I L R R V V D W R T P S L G T V N M E L R N V R S D D S A I Y F C G R V V D G F N A A G P L E F W G Q G S P V I 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
Q V V M T Q S P A T L S L S P G E T A A V S C R A S Q Y V D R S I S W Y Q L K T G R A P R L L V Y A A S S R S I G V P D R F S G S G S G R D F T L T I R G V Q S D D F A L Y Y C Q Q D Y Y W P V T F G Q G T R L D M K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

CDR Sequences (chothia definition)
CDRH1GYIFTDY
CDRH2NTNAGL
CDRH3VVDGFNAAGPLEF
CDRL1RASQYVDRSIS
CDRL2AASSRSI
CDRL3QQDYYWPVT

Orientation Angles (from ABangle)
HL-59.8°
HC173.66°
HC2115.23°
LC1119.61°
LC288.59°
dc15.98Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupunknown
Light subgroupunknown
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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 70A 70B 70C 70D 70E 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L I Q S G P Q F K T P G A S V T V S C K A S G Y I F T D Y L I H W V R L V P G K G L E W L G R I N T N A G L M Y L S H K F E G R L I L R R V V D W R T P S L G T V N M E L R N V R S D D S A I Y F C G R V V D G F N A A G P L E F W G Q G S P V I 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
Q V V M T Q S P A T L S L S P G E T A A V S C R A S Q Y V D R S I S W Y Q L K T G R A P R L L V Y A A S S R S I G V P D R F S G S G S G R D F T L T I R G V Q S D D F A L Y Y C Q Q D Y Y W P V T F G Q G T R L D M K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

CDR Sequences (chothia definition)
CDRH1GYIFTDY
CDRH2NTNAGL
CDRH3VVDGFNAAGPLEF
CDRL1RASQYVDRSIS
CDRL2AASSRSI
CDRL3QQDYYWPVT

Orientation Angles (from ABangle)
HL-59.84°
HC173.73°
HC2115.31°
LC1120.0°
LC288.47°
dc15.99Å
>   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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