Structure Viewer: 8a67

>   Structure details

Branched Lys48- and Lys63-Linked Tri-Ubiquitin (K48-K63-Ub3) in complex with Matured Synthetic Nanobody Nbsl3.3Q (3Rd Generation)

PDB8a67
SpeciesSYNTHETIC CONSTRUCT
MethodX-RAY DIFFRACTION
Resolution1.86Å
Number of Fvs2
In complexTrue
Light chain typeNA
Has constant regionFalse
>   Structure visualisation
Please note the WebGL plugin needs to be enabled to use PV Viewer.

Display options:














>   Fv information

This PDB has 2 Fv(s).

>   D/-
Fv Details
Heavy chainD
Light chain
Heavy subgroupIGHV1
Light subgroupNA
SpeciesSYNTHETIC CONSTRUCT
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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 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 100F 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G G G L V Q A G G S L R L S C A A S G S I F D L G V M G W Y R Q A P G K E R E Q V A G I D Y G G V T N Y A D S V K G R F T I S R D N D T V Y L Q M N S L K P E D T A V Y Y C A A G I V G D E V G W I Y Y L Y W G Q G T Q V T V S S

Antigen Details
Antigen chainsA,C,B
Antigen typeprotein
Antigen namepolyubiquitin-b
Antigen speciesHOMO SAPIENS
Antigen sequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR/MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG/MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG

CDR Sequences (chothia definition)
CDRH1GSIFDLG
CDRH2DYGGV
CDRH3GIVGDEVGWIYYLY

>   H/-
Fv Details
Heavy chainH
Light chain
Heavy subgroupIGHV1
Light subgroupNA
SpeciesSYNTHETIC CONSTRUCT
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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 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 100F 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G G G L V Q A G G S L R L S C A A S G S I F D L G V M G W Y R Q A P G K E R E Q V A G I D Y G G V T N Y A D S V K G R F T I S R D N D T V Y L Q M N S L K P E D T A V Y Y C A A G I V G D E V G W I Y Y L Y W G Q G T Q V T V S S

Antigen Details
Antigen chainsE,G,F
Antigen typeprotein
Antigen namepolyubiquitin-b
Antigen speciesHOMO SAPIENS
Antigen sequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR/MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG/MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG

CDR Sequences (chothia definition)
CDRH1GSIFDLG
CDRH2DYGGV
CDRH3GIVGDEVGWIYYLY

>   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]

Our privacy policy