Structure Viewer: 3cfi

>   Structure details

Nanobody-aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus

PDB3cfi
SpeciesLAMA GLAMA
MethodX-RAY DIFFRACTION
Resolution2.58Å
Number of Fvs4
In complexTrue
Light chain type
Has constant regionFalse
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>   Fv information

This PDB has 4 Fv(s).

>   L/-
Fv Details
Heavy chainL
Light chain
Heavy subgroupIGHV3
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
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 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 101 103 104 105 106 107 108 109 110 111 112
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G F A F S G Y A M S W V R Q A P G K G L E W V S G I N R D G S T S Y T A P V K G R F T I S R D N A K N I L Y L Q M N S L R P E D T A V Y Y C A K W L G G R D W Y D R G Q G T Q V T V S

Antigen Details
Antigen chainsK
Antigen typeprotein
Antigen nametype ii secretory pathway, pseudopilin epsj
Antigen speciesVIBRIO VULNIFICUS
Antigen sequenceNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWADYLLDSDNKGIMFARLGWHNPQQQFPRGEVTKVGYRIKDERLERVWWRYPDTPAGQEGVVTPLLSDVEELNVRFYDGKQWINEWSNELTLPAAISVELTLKDYGKIARTYLTPEGN

CDR Sequences (chothia definition)
CDRH1GFAFSGY
CDRH2NRDGS
CDRH3WLGGRDWYD

>   I/-
Fv Details
Heavy chainI
Light chain
Heavy subgroupIGHV3
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
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 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 101 103 104 105 106 107 108 109 110 111 112
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G F A F S G Y A M S W V R Q A P G K G L E W V S G I N R D G S T S Y T A P V K G R F T I S R D N A K N I L Y L Q M N S L R P E D T A V Y Y C A K W L G G R D W Y D R G Q G T Q V T V S

Antigen Details
Antigen chainsH
Antigen typeprotein
Antigen nametype ii secretory pathway, pseudopilin epsj
Antigen speciesVIBRIO VULNIFICUS
Antigen sequenceNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWADYLLDSDNKGIMFARLGWHNPQQQFPRGEVTKVGYRIKDERLERVWWRYPDTPAGQEGVVTPLLSDVEELNVRFYDGKQWINEWSNELTLPAAISVELTLKDYGKIARTYLTPEGN

CDR Sequences (chothia definition)
CDRH1GFAFSGY
CDRH2NRDGS
CDRH3WLGGRDWYD

>   C/-
Fv Details
Heavy chainC
Light chain
Heavy subgroupIGHV3
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
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 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 101 103 104 105 106 107 108 109 110 111 112
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G F A F S G Y A M S W V R Q A P G K G L E W V S G I N R D G S T S Y T A P V K G R F T I S R D N A K N I L Y L Q M N S L R P E D T A V Y Y C A K W L G G R D W Y D R G Q G T Q V T V S

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nametype ii secretory pathway, pseudopilin epsj
Antigen speciesVIBRIO VULNIFICUS
Antigen sequenceNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWADYLLDSDNKGIMFARLGWHNPQQQFPRGEVTKVGYRIKDERLERVWWRYPDTPAGQEGVVTPLLSDVEELNVRFYDGKQWINEWSNELTLPAAISVELTLKDYGKIARTYLTPEGN

CDR Sequences (chothia definition)
CDRH1GFAFSGY
CDRH2NRDGS
CDRH3WLGGRDWYD

>   F/-
Fv Details
Heavy chainF
Light chain
Heavy subgroupIGHV3
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
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 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 101 103 104 105 106 107 108 109 110 111 112
Q V Q L Q E S G G G L V Q P G G S L R L S C A A S G F A F S G Y A M S W V R Q A P G K G L E W V S G I N R D G S T S Y T A P V K G R F T I S R D N A K N I L Y L Q M N S L R P E D T A V Y Y C A K W L G G R D W Y D R G Q G T Q V T V S

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen nametype ii secretory pathway, pseudopilin epsj
Antigen speciesVIBRIO VULNIFICUS
Antigen sequenceNELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWADYLLDSDNKGIMFARLGWHNPQQQFPRGEVTKVGYRIKDERLERVWWRYPDTPAGQEGVVTPLLSDVEELNVRFYDGKQWINEWSNELTLPAAISVELTLKDYGKIARTYLTPEGN

CDR Sequences (chothia definition)
CDRH1GFAFSGY
CDRH2NRDGS
CDRH3WLGGRDWYD

>   Downloads

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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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