Structure Viewer: 5dub

>   Structure details

Context-independent anti-Hypusine antibody Fabhpu98 in complex with Deoxyhypusine

PDB5dub
SpeciesORYCTOLAGUS CUNICULUS
MethodX-RAY DIFFRACTION
Resolution2.0Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?True

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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E S V E E S G G R L V T P G T P L T L T C T V S G F S L S T Y T M N W V R Q A P G K G L E W I G D I Y T D G N T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T T E D T A T Y F C A R D S W D A S S Y Y G L D L W G Q G T L V T V S S

Light chain

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

Antigen Details
Antigen chainsP
Antigen typepeptide
Antigen namepeptide
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequenceGXGA

CDR Sequences (chothia definition)
CDRH1GFSLSTY
CDRH2YTDGN
CDRH3DSWDASSYYGLDL
CDRL1QASEDIKRYLA
CDRL2AASKLAS
CDRL3QQGYTSSNVNNA

Orientation Angles (from ABangle)
HL-49.69°
HC169.16°
HC2119.89°
LC1121.61°
LC282.0°
dc16.41Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?True

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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E S V E E S G G R L V T P G T P L T L T C T V S G F S L S T Y T M N W V R Q A P G K G L E W I G D I Y T D G N T Y Y A N W A K G R F T I S K T S T T V D L K I T S P T T E D T A T Y F C A R D S W D A S S Y Y G L D L W G Q G T L V T V S S

Light chain

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

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

CDR Sequences (chothia definition)
CDRH1GFSLSTY
CDRH2YTDGN
CDRH3DSWDASSYYGLDL
CDRL1QASEDIKRYLA
CDRL2AASKLAS
CDRL3QQGYTSSNVNNA

Orientation Angles (from ABangle)
HL-50.95°
HC169.21°
HC2119.84°
LC1121.1°
LC281.68°
dc16.49Å
>   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]

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