Structure Viewer: 8to9

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Cryo-Em Structure of Trnm-F*01 Fab in complex with Hiv-1 Env Trimer Conc Sosip

PDB8to9
SpeciesMACACA MULATTA
MethodELECTRON MICROSCOPY
Resolution4.03Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 3 Fv(s).

>   D/F
Fv Details
Heavy chainD
Light chainF
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 31A 31B 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 100D 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G V V K P S E T L S L T C A V S G D S I K S A Y Q Y W N W I R Q P R G K G P E W I G G V Y S S S D S T A Y N P S L E S R V S I S R D T S N N R F S L N L R S V T A T D T A T Y F C A R S V R D S R G W G R Y F L D T W G Q G L L V T 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
D I Q M T Q S P S S L S A S V G D T V T I T C R A S Q S I S T W L A W Y Q Q K P G K A P K V L I Y S A S I L Q S G V P S R F R G S G S G S D F T L T I G S L Q I E D F A T Y F C Q Q Y T G S P F T F G G G T K V E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHOMO SAPIENS
Antigen sequenceNLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNVNVTNTNNNNMKEEMKNCSFNTTTEIRDKKQKEYALFYRLDIVPLNENSSEYRLINCNTSTITQICPKVSFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTDNAKTIIVHLNESVEINCTRPNNMTRKSIRIGPGQTFYALGDIIGDIRQPHCNISEAKWNKTLQRVKKKLKEHFPNKTIKFAPSSGGDLEITTHSFNCRGEFFYCNTSKLFNSTYNNTTSNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGNNNNNTETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTKCKRRVVERRRRRR

CDR Sequences (chothia definition)
CDRH1GDSIKSAYQ
CDRH2YSSSDS
CDRH3SVRDSRGWGRYFLDT
CDRL1RASQSISTWLA
CDRL2SASILQS
CDRL3QQYTGSPFT

Orientation Angles (from ABangle)
HL-62.08°
HC174.43°
HC2119.06°
LC1119.67°
LC282.94°
dc16.84Å
>   E/G
Fv Details
Heavy chainE
Light chainG
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 31A 31B 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 100D 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G V V K P S E T L S L T C A V S G D S I K S A Y Q Y W N W I R Q P R G K G P E W I G G V Y S S S D S T A Y N P S L E S R V S I S R D T S N N R F S L N L R S V T A T D T A T Y F C A R S V R D S R G W G R Y F L D T W G Q G L L V T 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
D I Q M T Q S P S S L S A S V G D T V T I T C R A S Q S I S T W L A W Y Q Q K P G K A P K V L I Y S A S I L Q S G V P S R F R G S G S G S D F T L T I G S L Q I E D F A T Y F C Q Q Y T G S P F T F G G G T K V E I K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHOMO SAPIENS
Antigen sequenceNLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNVNVTNTNNNNMKEEMKNCSFNTTTEIRDKKQKEYALFYRLDIVPLNENSSEYRLINCNTSTITQICPKVSFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTDNAKTIIVHLNESVEINCTRPNNMTRKSIRIGPGQTFYALGDIIGDIRQPHCNISEAKWNKTLQRVKKKLKEHFPNKTIKFAPSSGGDLEITTHSFNCRGEFFYCNTSKLFNSTYNNTTSNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGNNNNNTETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTKCKRRVVERRRRRR

CDR Sequences (chothia definition)
CDRH1GDSIKSAYQ
CDRH2YSSSDS
CDRH3SVRDSRGWGRYFLDT
CDRL1RASQSISTWLA
CDRL2SASILQS
CDRL3QQYTGSPFT

Orientation Angles (from ABangle)
HL-62.35°
HC173.52°
HC2119.76°
LC1120.49°
LC282.62°
dc16.72Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 31A 31B 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 100D 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G V V K P S E T L S L T C A V S G D S I K S A Y Q Y W N W I R Q P R G K G P E W I G G V Y S S S D S T A Y N P S L E S R V S I S R D T S N N R F S L N L R S V T A T D T A T Y F C A R S V R D S R G W G R Y F L D T W G Q G L L V T 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
D I Q M T Q S P S S L S A S V G D T V T I T C R A S Q S I S T W L A W Y Q Q K P G K A P K V L I Y S A S I L Q S G V P S R F R G S G S G S D F T L T I G S L Q I E D F A T Y F C Q Q Y T G S P F T F G G G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHOMO SAPIENS
Antigen sequenceNLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCTNVNVTNTNNNNMKEEMKNCSFNTTTEIRDKKQKEYALFYRLDIVPLNENSSEYRLINCNTSTITQICPKVSFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTDNAKTIIVHLNESVEINCTRPNNMTRKSIRIGPGQTFYALGDIIGDIRQPHCNISEAKWNKTLQRVKKKLKEHFPNKTIKFAPSSGGDLEITTHSFNCRGEFFYCNTSKLFNSTYNNTTSNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGNNNNNTETFRPGGGDMRDNWRSELYKYKVVEIKPLGIAPTKCKRRVVERRRRRR

CDR Sequences (chothia definition)
CDRH1GDSIKSAYQ
CDRH2YSSSDS
CDRH3SVRDSRGWGRYFLDT
CDRL1RASQSISTWLA
CDRL2SASILQS
CDRL3QQYTGSPFT

Orientation Angles (from ABangle)
HL-62.19°
HC173.96°
HC2119.31°
LC1119.87°
LC282.5°
dc16.8Å
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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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