Structure Viewer: 6vpx

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Nanodisc of Full-Length Hiv-1 Envelope Glycoprotein Clone amc011 in complex with One Pgt151 Fab and Three 10E8 Fabs

PDB6vpx
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution5.0Å
Number of Fvs4
In complexTrue
Light chain typeKappa,Lambda
Has constant regionFalse
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>   Fv information

This PDB has 4 Fv(s).

>   P/Q
Fv Details
Heavy chainP
Light chainQ
Heavy subgroupIGHV3
Light subgroupIGKV2
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

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 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 100N 100O 100P 100Q 100R 101 102 103 104 105 106 107 108 109 110 111 112 113
V Q L V E S G G G V V Q P G K S V R L S C V V S D F P F S K Y P M Y W V R Q A P G K G L E W V A A I S G D A W H V V Y S N S V Q G R F L V S R D N V K N T L Y L E M N S L K I E D T A V Y R C A R M F Q E S G P P R L D R W S G R N Y Y Y Y S G M D V W G Q G T T V T V S S

Light chain

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 30A 30B 30C 30D 30E 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
I V M T Q T P L S L S V T P G Q P A S I S C K S S E S L R Q S N G K T S L Y W Y R Q K P G Q S P Q L L V F E V S N R F S G V S D R F V G S G S G T D F T L R I S R V E A E D V G F Y Y C M Q S K D F P L T F G G G T K V D

Antigen Details
Antigen chainsD,C,B
Antigen typeprotein
Antigen nameenvelope glycoprotein gp41; envelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARLLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNTSWSNKSYNQIWNNMTWMEWEREIDNYTSLIYTLIEDSQNQQEKNEQELLELD/AVGIGAVFLGFLGAAGSTMGAASMTLTVQARLLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNTSWSNKSYNQIWNNMTWMEWEREIDNYTSLIYTLIEDSQNQQEKNEQELLELD/AEQLWVTVYYGVPVWKEATTTLFCASDARAYDTEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNSSSGEKMEGGEIKNCSFNITTSMRDKVQKEYALFYKLDVVPIKNDNTSYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKIIIVQLNKSVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISGTKWNDTLKQIVVKLKEQFGNKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEGSNNTKGNGTIVLPCRIKQIVNMWQEVGKAMYAPPIKGQIRCSSNITGLILIRDGGNNNESTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGIAPTKAKRRVVQ

CDR Sequences (chothia definition)
CDRH1DFPFSKY
CDRH2SGDAWH
CDRH3MFQESGPPRLDRWSGRNYYYYSGMDV
CDRL1KSSESLRQSNGKTSLY
CDRL2EVSNRFS
CDRL3MQSKDFPLT

Orientation Angles (from ABangle)
HL-57.83°
HC171.86°
HC2117.14°
LC1118.84°
LC283.77°
dc17.05Å
>   M/O
Fv Details
Heavy chainM
Light chainO
Heavy subgroupIGHV3
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 52A 52B 52C 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 101 102 103 104 105 106 107 108 109 110 111
E V Q L V E S G G G L V K P G G S L R L S C S A S G F D F D N A W M T W V R Q P P G K G L E W V G R I T G P G E G W S V D Y A A P V E G R F T I S R L N S I N F L Y L E M N N L R M E D S G L Y F C A R T G K Y Y D F W S G Y P P G E E Y F Q D W G R G T L V T V

Light chain

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 95C 96 97 98 99 100 101 102 103 104 105 106 107
Y E L T Q E T G V S V A L G R T V T I T C R G D S L R S H Y A S W Y Q K K P G Q A P I L L F Y G K N N R P S G V P D R F S G S A S G N R A S L T I S G A Q A E D D A E Y Y C S S R D K S G S R L S V F G G G T K L T V L

Antigen Details
Antigen chainsJ,E,F
Antigen typeprotein
Antigen namemper peptide; envelope glycoprotein gp120; envelope glycoprotein gp41
Antigen specieshomo sapiens ; human immunodeficiency virus 1 ; human immunodeficiency virus 1
Antigen sequenceNWFDITNVLWWIKAVIQ/AVGIGAVFLGFLGAAGSTMGAASMTLTVQARLLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNTSWSNKSYNQIWNNMTWMEWEREIDNYTSLIYTLIEDSQNQQEKNEQELLELD/AEQLWVTVYYGVPVWKEATTTLFCASDARAYDTEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNSSSGEKMEGGEIKNCSFNITTSMRDKVQKEYALFYKLDVVPIKNDNTSYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKIIIVQLNKSVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISGTKWNDTLKQIVVKLKEQFGNKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEGSNNTKGNGTIVLPCRIKQIVNMWQEVGKAMYAPPIKGQIRCSSNITGLILIRDGGNNNESTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGIAPTKAKRRVVQ

CDR Sequences (chothia definition)
CDRH1GFDFDNA
CDRH2TGPGEGWS
CDRH3TGKYYDFWSGYPPGEEYFQD
CDRL1RGDSLRSHYAS
CDRL2GKNNRPS
CDRL3SSRDKSGSRLSV

Orientation Angles (from ABangle)
HL-61.85°
HC170.2°
HC2120.74°
LC1118.96°
LC281.27°
dc15.84Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 52A 52B 52C 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 101 102 103 104 105 106 107 108 109 110 111
E V Q L V E S G G G L V K P G G S L R L S C S A S G F D F D N A W M T W V R Q P P G K G L E W V G R I T G P G E G W S V D Y A A P V E G R F T I S R L N S I N F L Y L E M N N L R M E D S G L Y F C A R T G K Y Y D F W S G Y P P G E E Y F Q D W G R G T L V T V

Light chain

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 95C 96 97 98 99 100 101 102 103 104 105 106 107
Y E L T Q E T G V S V A L G R T V T I T C R G D S L R S H Y A S W Y Q K K P G Q A P I L L F Y G K N N R P S G V P D R F S G S A S G N R A S L T I S G A Q A E D D A E Y Y C S S R D K S G S R L S V F G G G T K L T V L

Antigen Details
Antigen chainsG
Antigen typepeptide
Antigen namemper peptide
Antigen speciesHOMO SAPIENS
Antigen sequenceNWFDITNVLWWIKAVIQ

CDR Sequences (chothia definition)
CDRH1GFDFDNA
CDRH2TGPGEGWS
CDRH3TGKYYDFWSGYPPGEEYFQD
CDRL1RGDSLRSHYAS
CDRL2GKNNRPS
CDRL3SSRDKSGSRLSV

Orientation Angles (from ABangle)
HL-61.85°
HC170.2°
HC2120.74°
LC1118.96°
LC281.27°
dc15.84Å
>   K/N
Fv Details
Heavy chainK
Light chainN
Heavy subgroupIGHV3
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 52A 52B 52C 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 101 102 103 104 105 106 107 108 109 110 111
E V Q L V E S G G G L V K P G G S L R L S C S A S G F D F D N A W M T W V R Q P P G K G L E W V G R I T G P G E G W S V D Y A A P V E G R F T I S R L N S I N F L Y L E M N N L R M E D S G L Y F C A R T G K Y Y D F W S G Y P P G E E Y F Q D W G R G T L V T V

Light chain

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 95C 96 97 98 99 100 101 102 103 104 105 106 107
Y E L T Q E T G V S V A L G R T V T I T C R G D S L R S H Y A S W Y Q K K P G Q A P I L L F Y G K N N R P S G V P D R F S G S A S G N R A S L T I S G A Q A E D D A E Y Y C S S R D K S G S R L S V F G G G T K L T V L

Antigen Details
Antigen chainsI,A
Antigen typeprotein
Antigen namemper peptide; envelope glycoprotein gp120
Antigen specieshomo sapiens ; human immunodeficiency virus 1
Antigen sequenceNWFDITNVLWWIKAVIQ/AEQLWVTVYYGVPVWKEATTTLFCASDARAYDTEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNSSSGEKMEGGEIKNCSFNITTSMRDKVQKEYALFYKLDVVPIKNDNTSYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKIIIVQLNKSVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISGTKWNDTLKQIVVKLKEQFGNKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEGSNNTKGNGTIVLPCRIKQIVNMWQEVGKAMYAPPIKGQIRCSSNITGLILIRDGGNNNESTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGIAPTKAKRRVVQ

CDR Sequences (chothia definition)
CDRH1GFDFDNA
CDRH2TGPGEGWS
CDRH3TGKYYDFWSGYPPGEEYFQD
CDRL1RGDSLRSHYAS
CDRL2GKNNRPS
CDRL3SSRDKSGSRLSV

Orientation Angles (from ABangle)
HL-61.85°
HC170.2°
HC2120.74°
LC1118.96°
LC281.27°
dc15.84Å
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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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