Structure Viewer: 5tkj

>   Structure details

Structure of Vaccine-Elicited Diverse Hiv-1 Neutralizing antibody Vfp1.01 in complex with Hiv-1 Fusion Peptide Residue 512-519

PDB5tkj
SpeciesMUS MUSCULUS
MethodX-RAY DIFFRACTION
Resolution2.118Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   J/K
Fv Details
Heavy chainJ
Light chainK
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q S G T E L V W P G T S V T L S C K A S G Y T F T D Y E I H W V K Q T P V H G L E W I G A I V P K T G Y T A Y N Q K F R G K A I L T A D K S S S T A Y M D L R R L T S E D S A V Y Y C T R L R N Y W Y F D V W G T G T T V T V S P

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

Antigen Details
Antigen chainsL
Antigen typepeptide
Antigen namehiv-1 fusion peptide residue 512-519
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVF

CDR Sequences (chothia definition)
CDRH1GYTFTDY
CDRH2VPKTGY
CDRH3LRNYWYFDV
CDRL1RSSQSIVYSDGNTYLE
CDRL2KVSNRFS
CDRL3FQGSHVPYT

Orientation Angles (from ABangle)
HL-55.49°
HC172.22°
HC2118.12°
LC1126.17°
LC282.18°
dc15.92Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q S G T E L V W P G T S V T L S C K A S G Y T F T D Y E I H W V K Q T P V H G L E W I G A I V P K T G Y T A Y N Q K F R G K A I L T A D K S S S T A Y M D L R R L T S E D S A V Y Y C T R L R N Y W Y F D V W G T G T T V T V S P

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

Antigen Details
Antigen chainsC
Antigen typepeptide
Antigen namehiv-1 fusion peptide residue 512-519
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVF

CDR Sequences (chothia definition)
CDRH1GYTFTDY
CDRH2VPKTGY
CDRH3LRNYWYFDV
CDRL1RSSQSIVYSDGNTYLE
CDRL2KVSNRFS
CDRL3FQGSHVPYT

Orientation Angles (from ABangle)
HL-55.33°
HC172.22°
HC2118.71°
LC1125.92°
LC282.21°
dc15.95Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q S G T E L V W P G T S V T L S C K A S G Y T F T D Y E I H W V K Q T P V H G L E W I G A I V P K T G Y T A Y N Q K F R G K A I L T A D K S S S T A Y M D L R R L T S E D S A V Y Y C T R L R N Y W Y F D V W G T G T T V T V S P

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

Antigen Details
Antigen chainsI
Antigen typepeptide
Antigen namehiv-1 fusion peptide residue 512-519
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVF

CDR Sequences (chothia definition)
CDRH1GYTFTDY
CDRH2VPKTGY
CDRH3LRNYWYFDV
CDRL1RSSQSIVYSDGNTYLE
CDRL2KVSNRFS
CDRL3FQGSHVPYT

Orientation Angles (from ABangle)
HL-56.09°
HC171.84°
HC2117.84°
LC1126.12°
LC282.15°
dc15.89Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesMUS MUSCULUS
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q S G T E L V W P G T S V T L S C K A S G Y T F T D Y E I H W V K Q T P V H G L E W I G A I V P K T G Y T A Y N Q K F R G K A I L T A D K S S S T A Y M D L R R L T S E D S A V Y Y C T R L R N Y W Y F D V W G T G T T V T V S P

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

Antigen Details
Antigen chainsF
Antigen typepeptide
Antigen namehiv-1 fusion peptide residue 512-519
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVF

CDR Sequences (chothia definition)
CDRH1GYTFTDY
CDRH2VPKTGY
CDRH3LRNYWYFDV
CDRL1RSSQSIVYSDGNTYLE
CDRL2KVSNRFS
CDRL3FQGSHVPYT

Orientation Angles (from ABangle)
HL-55.38°
HC172.16°
HC2118.64°
LC1125.88°
LC282.19°
dc15.96Å
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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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