Structure Viewer: 8tl3

>   Structure details

Cryo-Em Structure of Hiv-1 Bg505Ds-Sosip.664 Env Trimer Bound to Dj85-D.01 Fab

PDB8tl3
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.1Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
>   Structure visualisation
Please note the WebGL plugin needs to be enabled to use PV Viewer.

Display options:














>   Fv information

This PDB has 3 Fv(s).

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

Antigen Details
Antigen chainsB,A
Antigen typeprotein
Antigen namebg505 ds-sosip glycoprotein gp41; bg505 ds-sosip glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GASISGNY
CDRH2HGNGAT
CDRH3QFRTYVGSHLFSYSDF
CDRL1RASQDITTDLN
CDRL2VASSLQN
CDRL3LQYDSYPWT

Orientation Angles (from ABangle)
HL-58.07°
HC171.68°
HC2119.26°
LC1119.9°
LC281.72°
dc16.92Å
>   I/J
Fv Details
Heavy chainI
Light chainJ
Heavy subgroupIGHV4
Light subgroupIGKV1
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 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 100H 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L H E S G P G L V K P S E T L S L T C A V S G A S I S G N Y Y W N W I R Q S P G R G L E W I G N I H G N G A T T Q Y N P S L K S R V T I S Q D T S K N Q V F L N L N S M T A A D T A I Y Y C A T Q F R T Y V G S H L F S Y S D F W G Q G V 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 R V T M T C R A S Q D I T T D L N W Y Q Q K P G Q P P K L L I Y V A S S L Q N G V P S R F S G S G S G T E F T L T I R S L Q P E D F A T Y Y C L Q Y D S Y P W T F G Q G T T V D F R

Antigen Details
Antigen chainsD,C
Antigen typeprotein
Antigen namebg505 ds-sosip glycoprotein gp41; bg505 ds-sosip glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GASISGNY
CDRH2HGNGAT
CDRH3QFRTYVGSHLFSYSDF
CDRL1RASQDITTDLN
CDRL2VASSLQN
CDRL3LQYDSYPWT

Orientation Angles (from ABangle)
HL-57.96°
HC171.71°
HC2119.41°
LC1120.11°
LC281.86°
dc16.81Å
>   K/L
Fv Details
Heavy chainK
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV1
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 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 100H 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L H E S G P G L V K P S E T L S L T C A V S G A S I S G N Y Y W N W I R Q S P G R G L E W I G N I H G N G A T T Q Y N P S L K S R V T I S Q D T S K N Q V F L N L N S M T A A D T A I Y Y C A T Q F R T Y V G S H L F S Y S D F W G Q G V 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 R V T M T C R A S Q D I T T D L N W Y Q Q K P G Q P P K L L I Y V A S S L Q N G V P S R F S G S G S G T E F T L T I R S L Q P E D F A T Y Y C L Q Y D S Y P W T F G Q G T T V D F R

Antigen Details
Antigen chainsF,E
Antigen typeprotein
Antigen namebg505 ds-sosip glycoprotein gp41; bg505 ds-sosip glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GASISGNY
CDRH2HGNGAT
CDRH3QFRTYVGSHLFSYSDF
CDRL1RASQDITTDLN
CDRL2VASSLQN
CDRL3LQYDSYPWT

Orientation Angles (from ABangle)
HL-57.9°
HC171.29°
HC2119.67°
LC1120.05°
LC281.54°
dc16.94Å
>   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]

Our privacy policy