Structure Viewer: 5jyl

>   Structure details

Human P-Cadherin Mec1 with Scfv Tsp7 Bound

PDB5jyl
SpeciesMUS MUSCULUS
MethodX-RAY DIFFRACTION
Resolution2.55Å
Number of Fvs2
In complexTrue
Light chain typeunknown
Has constant regionFalse
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>   Fv information

This PDB has 2 Fv(s).

>   D/D
Fv Details
Heavy chainD
Light chainD
Heavy subgroupunknown
Light subgroupunknown
SpeciesMUS MUSCULUS
In complex?True
scFv?True
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P E L V K P G A S V K M S C K A S G Y S F T A Y N M H W V K Q S H G K S L E W I G F I D P Y S G I I T Y N Q T F K G K A T L T V D K S S S T A Y M Q L N S L T S E D S A V Y Y C A R R G Y Y D G G F D Y W G Q G T T L 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 M T Q T T S S L S A S L G D R V T I S C R A S Q D I T N Y L N W Y Q Q K P D G T V K L L I Y Y T S R L H S G V P S R F S G S G S G T D Y S L T I S N L E Q E D I A T Y F C Q Q D S K H P R T F G G G T K L E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namecadherin-3
Antigen speciesHOMO SAPIENS
Antigen sequenceMDWVVAPISVPENGKGPFPQRLNQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTD

CDR Sequences (chothia definition)
CDRH1GYSFTAY
CDRH2DPYSGI
CDRH3RGYYDGGFDY
CDRL1RASQDITNYLN
CDRL2YTSRLHS
CDRL3QQDSKHPRT

Orientation Angles (from ABangle)
HL-63.58°
HC169.9°
HC2111.05°
LC1120.61°
LC280.85°
dc15.86Å
>   B/B
Fv Details
Heavy chainB
Light chainB
Heavy subgroupunknown
Light subgroupunknown
SpeciesMUS MUSCULUS
In complex?True
scFv?True
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P E L V K P G A S V K M S C K A S G Y S F T A Y N M H W V K Q S H G K S L E W I G F I D P Y S G I I T Y N Q T F K G K A T L T V D K S S S T A Y M Q L N S L T S E D S A V Y Y C A R R G Y Y D G G F D Y W G Q G T T L 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 M T Q T T S S L S A S L G D R V T I S C R A S Q D I T N Y L N W Y Q Q K P D G T V K L L I Y Y T S R L H S G V P S R F S G S G S G T D Y S L T I S N L E Q E D I A T Y F C Q Q D S K H P R T F G G G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namecadherin-3
Antigen speciesHOMO SAPIENS
Antigen sequenceMDWVVAPISVPENGKGPFPQRLNQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTD

CDR Sequences (chothia definition)
CDRH1GYSFTAY
CDRH2DPYSGI
CDRH3RGYYDGGFDY
CDRL1RASQDITNYLN
CDRL2YTSRLHS
CDRL3QQDSKHPRT

Orientation Angles (from ABangle)
HL-64.46°
HC170.12°
HC2111.09°
LC1121.06°
LC280.13°
dc15.7Å
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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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