Structure Viewer: 6o2a

>   Structure details

Crystal Structure of 4493 Fab in complex with Circumsporozoite Protein Ndn and anti-Kappa Vhh Domain

PDB6o2a
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.15Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV3
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 52A 52B 52C 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 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 R S L R L S C T A S G F T F G D Y A M S W V R Q A P G K G L E W V G F I R S K A N G G R T E N P A S V K G R F T I S R D D S K S I A Y L Q M N S L K T E D T A V Y Y C T R V E L G S S W S L G Y 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 30A 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 G T L S L S P G E R A T L S C R A S Q S V S S T Y L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q Y G S S P W T F G Q G T K V E I K

Antigen Details
Antigen chainsG,N
Antigen typeprotein
Antigen namecircumsporozoite protein; anti-kappa vhh domain
Antigen speciesplasmodium falciparum ; lama glama
Antigen sequenceNANPNVDPNANP/XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXXXDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVSS

CDR Sequences (chothia definition)
CDRH1GFTFGDY
CDRH2RSKANGGR
CDRH3VELGSSWSLGY
CDRL1RASQSVSSTYLA
CDRL2GASSRAT
CDRL3QQYGSSPWT

Orientation Angles (from ABangle)
HL-60.99°
HC171.03°
HC2119.67°
LC1118.9°
LC285.68°
dc16.21Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV3
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 52A 52B 52C 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 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 R S L R L S C T A S G F T F G D Y A M S W V R Q A P G K G L E W V G F I R S K A N G G R T E N P A S V K G R F T I S R D D S K S I A Y L Q M N S L K T E D T A V Y Y C T R V E L G S S W S L G Y 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 30A 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 G T L S L S P G E R A T L S C R A S Q S V S S T Y L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q Y G S S P W T F G Q G T K V E I K

Antigen Details
Antigen chainsF
Antigen typepeptide
Antigen namecircumsporozoite protein
Antigen speciesPLASMODIUM FALCIPARUM
Antigen sequenceNANPNVDPNANP

CDR Sequences (chothia definition)
CDRH1GFTFGDY
CDRH2RSKANGGR
CDRH3VELGSSWSLGY
CDRL1RASQSVSSTYLA
CDRL2GASSRAT
CDRL3QQYGSSPWT

Orientation Angles (from ABangle)
HL-60.74°
HC171.13°
HC2119.4°
LC1120.41°
LC285.7°
dc16.03Å
>   H/I
Fv Details
Heavy chainH
Light chainI
Heavy subgroupIGHV3
Light subgroupIGKV3
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 52A 52B 52C 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 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 R S L R L S C T A S G F T F G D Y A M S W V R Q A P G K G L E W V G F I R S K A N G G R T E N P A S V K G R F T I S R D D S K S I A Y L Q M N S L K T E D T A V Y Y C T R V E L G S S W S L G Y 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 30A 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 G T L S L S P G E R A T L S C R A S Q S V S S T Y L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q Y G S S P W T F G Q G T K V E I K

Antigen Details
Antigen chainsK
Antigen typepeptide
Antigen namecircumsporozoite protein
Antigen speciesPLASMODIUM FALCIPARUM
Antigen sequenceNANPNVDPNANP

CDR Sequences (chothia definition)
CDRH1GFTFGDY
CDRH2RSKANGGR
CDRH3VELGSSWSLGY
CDRL1RASQSVSSTYLA
CDRL2GASSRAT
CDRL3QQYGSSPWT

Orientation Angles (from ABangle)
HL-63.25°
HC171.29°
HC2119.86°
LC1118.72°
LC284.16°
dc16.04Å
>   O/P
Fv Details
Heavy chainO
Light chainP
Heavy subgroupIGHV3
Light subgroupIGKV3
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 52A 52B 52C 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 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 R S L R L S C T A S G F T F G D Y A M S W V R Q A P G K G L E W V G F I R S K A N G G R T E N P A S V K G R F T I S R D D S K S I A Y L Q M N S L K T E D T A V Y Y C T R V E L G S S W S L G Y 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 30A 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 G T L S L S P G E R A T L S C R A S Q S V S S T Y L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q Y G S S P W T F G Q G T K V E I K

Antigen Details
Antigen chainsL,M
Antigen typeprotein
Antigen namecircumsporozoite protein; anti-kappa vhh domain
Antigen speciesplasmodium falciparum ; lama glama
Antigen sequenceNANPNVDPNANP/XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXXXDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVSS

CDR Sequences (chothia definition)
CDRH1GFTFGDY
CDRH2RSKANGGR
CDRH3VELGSSWSLGY
CDRL1RASQSVSSTYLA
CDRL2GASSRAT
CDRL3QQYGSSPWT

Orientation Angles (from ABangle)
HL-62.31°
HC170.82°
HC2118.74°
LC1119.76°
LC285.99°
dc16.34Å
>   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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