Structure Viewer: 2ybr

>   Structure details

Crystal Structure of the Human Derived Single Chain antibody Fragment (Scfv) 9004G in complex with Cn2 toxin From the Scorpion Centruroides Noxius Hoffmann

PDB2ybr
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.55Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 3 Fv(s).

>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?True
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C T G S G F T F D N Y A M H W L R Q V P G E G L E W V S G I S R S S G D I D Y A D S V K G R F T I S R D D A K K T L S L Q M N S L R A E D T A V Y Y C A R G G V G S F D T W G Q G T M 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
E I V L T Q S P A T L S V S P G E R A T L S C R A S Q S V R S Y L A W Y Q Q K P G Q A P R L L F S D A S N R A T G I P A R F T G S G S G T D F T L T I S S L E P E D F A I Y Y C Q Q Y R Y S P R T F G Q G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namebeta-mammal toxin cn2
Antigen speciesCENTRUROIDES NOXIUS HOFFMANN
Antigen sequenceKEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS

CDR Sequences (chothia definition)
CDRH1GFTFDNY
CDRH2SRSSGD
CDRH3GGVGSFDT
CDRL1RASQSVRSYLA
CDRL2DASNRAT
CDRL3QQYRYSPRT

Orientation Angles (from ABangle)
HL-62.45°
HC173.52°
HC2117.87°
LC1117.75°
LC287.73°
dc16.36Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?True
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C T G S G F T F D N Y A M H W L R Q V P G E G L E W V S G I S R S S G D I D Y A D S V K G R F T I S R D D A K K T L S L Q M N S L R A E D T A V Y Y C A R G G V G S F D T W G Q G T M 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
E I V L T Q S P A T L S V S P G E R A T L S C R A S Q S V R S Y L A W Y Q Q K P G Q A P R L L F S D A S N R A T G I P A R F T G S G S G T D F T L T I S S L E P E D F A I Y Y C Q Q Y R Y S P R T F G Q G T K V E I K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namebeta-mammal toxin cn2
Antigen speciesCENTRUROIDES NOXIUS HOFFMANN
Antigen sequenceKEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS

CDR Sequences (chothia definition)
CDRH1GFTFDNY
CDRH2SRSSGD
CDRH3GGVGSFDT
CDRL1RASQSVRSYLA
CDRL2DASNRAT
CDRL3QQYRYSPRT

Orientation Angles (from ABangle)
HL-63.11°
HC173.07°
HC2117.78°
LC1119.56°
LC287.06°
dc16.27Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?True
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C T G S G F T F D N Y A M H W L R Q V P G E G L E W V S G I S R S S G D I D Y A D S V K G R F T I S R D D A K K T L S L Q M N S L R A E D T A V Y Y C A R G G V G S F D T W G Q G T M 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
E I V L T Q S P A T L S V S P G E R A T L S C R A S Q S V R S Y L A W Y Q Q K P G Q A P R L L F S D A S N R A T G I P A R F T G S G S G T D F T L T I S S L E P E D F A I Y Y C Q Q Y R Y S P R T F G Q G T K V E I K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen namebeta-mammal toxin cn2
Antigen speciesCENTRUROIDES NOXIUS HOFFMANN
Antigen sequenceKEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS

CDR Sequences (chothia definition)
CDRH1GFTFDNY
CDRH2SRSSGD
CDRH3GGVGSFDT
CDRL1RASQSVRSYLA
CDRL2DASNRAT
CDRL3QQYRYSPRT

Orientation Angles (from ABangle)
HL-62.83°
HC173.07°
HC2117.25°
LC1119.0°
LC288.24°
dc16.35Å
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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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