Structure Viewer: 5i8c

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Crystal Structure of Hiv-1 Clade a Bg505 Fusion Peptide (Residue 512-520) in complex with Broadly Neutralizing antibody Vrc34.01 Fab

PDB5i8c
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution1.54Å
Number of Fvs1
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 1 Fv(s).

>   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

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

Antigen Details
Antigen chainsC
Antigen typepeptide
Antigen namehiv-1 clade a bg505 fusion peptide (residue 512-520)
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFL

CDR Sequences (chothia definition)
CDRH1GYTFTGN
CDRH2NPHSGD
CDRH3DKYYGNEAVGMDV
CDRL1RASQGVRNELA
CDRL2YASTLQS
CDRL3QHMSSYPLT

Orientation Angles (from ABangle)
HL-60.59°
HC170.71°
HC2116.58°
LC1120.16°
LC283.22°
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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