Principles and Pitfalls in Designing Site Directed Peptide Ligands
| PDB | 1mck |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.7Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Lambda |
| Has constant region | True |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | |
| Light chain | A |
| Heavy subgroup | |
| Light subgroup | IGLV2 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (chothia) |
|---|
Light chain
| 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 30A | 30B | 30C | 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 | 95A | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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| S | A | L | T | Q | P | P | S | A | S | G | S | L | G | Q | S | V | T | I | S | C | T | G | T | S | S | D | V | G | G | Y | N | Y | V | S | W | Y | Q | Q | H | A | G | K | A | P | K | V | I | I | Y | E | V | N | K | R | P | S | G | V | P | D | R | F | S | G | S | K | S | G | N | T | A | S | L | T | V | S | G | L | Q | A | E | D | E | A | D | Y | Y | C | S | S | Y | E | G | S | D | N | F | V | F | G | T | G | T | K | V | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | P |
| Antigen type | peptide |
| Antigen name | peptide n-acetyl-d-glu-l-his-d-pro-nh2 |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | XEHPX |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRL1 | TGTSSDVGGYNYVS |
| CDRL2 | EVNKRPS |
| CDRL3 | SSYEGSDNFV |
| Fv Details | |
|---|---|
| Heavy chain | |
| Light chain | B |
| Heavy subgroup | |
| Light subgroup | IGLV2 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (chothia) |
|---|
Light chain
| 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 30A | 30B | 30C | 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 | 95A | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S | A | L | T | Q | P | P | S | A | S | G | S | L | G | Q | S | V | T | I | S | C | T | G | T | S | S | D | V | G | G | Y | N | Y | V | S | W | Y | Q | Q | H | A | G | K | A | P | K | V | I | I | Y | E | V | N | K | R | P | S | G | V | P | D | R | F | S | G | S | K | S | G | N | T | A | S | L | T | V | S | G | L | Q | A | E | D | E | A | D | Y | Y | C | S | S | Y | E | G | S | D | N | F | V | F | G | T | G | T | K | V | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | P |
| Antigen type | peptide |
| Antigen name | peptide n-acetyl-d-glu-l-his-d-pro-nh2 |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | XEHPX |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRL1 | TGTSSDVGGYNYVS |
| CDRL2 | EVNKRPS |
| CDRL3 | SSYEGSDNFV |
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]
