Structure Viewer: 6med

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Broadly Neutralizing antibodies against Hcv Use a Cdrh3 Disulfide Motif to Recognize an E2 Glycoprotein Site That Can Be Targeted For Vaccine Design

PDB6med
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.04Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   G/I
Fv Details
Heavy chainG
Light chainI
Heavy subgroupIGHV1
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G S S V K V S C K A S G G T L N S Y E I T W V R Q A P G Q G L E W M G G I T P I F E T T Y A Q K F Q G R V T I T A D E S T S T T Y M E L S S L R P E D T A V Y Y C A R D G V R Y C G G G R C Y N W F D P W G Q G T 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 I T C R A G Q N I N N Y L N W Y Q Q K P G K A P K V L I Y A A S N L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S H S T V R T F G Q G T K V E I K

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GGTLNSY
CDRH2TPIFE
CDRH3DGVRYCGGGRCYNWFDP
CDRL1RAGQNINNYLN
CDRL2AASNLQS
CDRL3QQSHSTVRT

Orientation Angles (from ABangle)
HL-52.49°
HC172.74°
HC2119.94°
LC1122.85°
LC280.5°
dc16.26Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G S S V K V S C K A S G G T L N S Y E I T W V R Q A P G Q G L E W M G G I T P I F E T T Y A Q K F Q G R V T I T A D E S T S T T Y M E L S S L R P E D T A V Y Y C A R D G V R Y C G G G R C Y N W F D P W G Q G T 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 I T C R A G Q N I N N Y L N W Y Q Q K P G K A P K V L I Y A A S N L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S H S T V R T F G Q G T K V E I K

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GGTLNSY
CDRH2TPIFE
CDRH3DGVRYCGGGRCYNWFDP
CDRL1RAGQNINNYLN
CDRL2AASNLQS
CDRL3QQSHSTVRT

Orientation Angles (from ABangle)
HL-55.53°
HC172.15°
HC2119.69°
LC1122.36°
LC279.91°
dc16.21Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV1
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G S S V K V S C K A S G G T L N S Y E I T W V R Q A P G Q G L E W M G G I T P I F E T T Y A Q K F Q G R V T I T A D E S T S T T Y M E L S S L R P E D T A V Y Y C A R D G V R Y C G G G R C Y N W F D P W G Q G T 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 I T C R A G Q N I N N Y L N W Y Q Q K P G K A P K V L I Y A A S N L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S H S T V R T F G Q G T K V E I K

Antigen Details
Antigen chains
Antigen type
Antigen name
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GGTLNSY
CDRH2TPIFE
CDRH3DGVRYCGGGRCYNWFDP
CDRL1RAGQNINNYLN
CDRL2AASNLQS
CDRL3QQSHSTVRT

Orientation Angles (from ABangle)
HL-53.35°
HC172.99°
HC2119.77°
LC1122.55°
LC280.49°
dc16.22Å
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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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