Crystal Structure of Cd8alpha-Beta in complex with Yts 156.7 Fab
| PDB | 3b9k |
| Species | RATTUS RATTUS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.7Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Kappa |
| Has constant region | True |
|
|
Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV2 |
| Light subgroup | IGKV19 |
| Species | RATTUS RATTUS |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | R | L | Q | E | S | G | P | G | L | V | Q | P | S | Q | T | L | S | L | T | C | S | V | S | G | F | S | L | I | S | D | S | V | H | W | V | R | Q | P | P | G | K | G | L | E | W | M | G | G | I | W | A | D | G | S | T | E | Y | N | S | A | L | K | S | R | L | S | I | S | R | D | T | S | K | S | Q | G | F | L | K | M | N | S | L | Q | T | D | D | T | A | I | Y | F | C | T | S | N | R | E | S | Y | Y | F | D | Y | W | G | Q | G | T | M | 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 | 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 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | I | K | M | T | Q | S | P | A | S | L | S | A | S | L | G | D | K | V | T | I | T | C | Q | A | S | Q | N | I | D | K | Y | I | A | W | Y | Q | Q | K | P | G | K | A | P | R | Q | L | I | H | Y | T | S | T | L | V | S | G | T | P | S | R | F | S | G | S | G | S | G | R | D | Y | T | F | S | I | S | S | V | E | S | E | D | I | A | S | Y | Y | C | L | Q | Y | D | T | L | Y | T | F | G | A | G | T | K | L | E | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | B |
| Antigen type | protein |
| Antigen name | t-cell surface glycoprotein cd8 beta chain |
| Antigen species | MUS MUSCULUS |
| Antigen sequence | LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDVSSADLVPR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSLISD |
| CDRH2 | WADGS |
| CDRH3 | NRESYYFDY |
| CDRL1 | QASQNIDKYIA |
| CDRL2 | YTSTLVS |
| CDRL3 | LQYDTLYT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -55.86° |
| HC1 | 73.27° |
| HC2 | 121.39° |
| LC1 | 122.03° |
| LC2 | 78.96° |
| dc | 16.23Å |
| Fv Details | |
|---|---|
| Heavy chain | D |
| Light chain | C |
| Heavy subgroup | IGHV2 |
| Light subgroup | IGKV19 |
| Species | RATTUS RATTUS |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | R | L | Q | E | S | G | P | G | L | V | Q | P | S | Q | T | L | S | L | T | C | S | V | S | G | F | S | L | I | S | D | S | V | H | W | V | R | Q | P | P | G | K | G | L | E | W | M | G | G | I | W | A | D | G | S | T | E | Y | N | S | A | L | K | S | R | L | S | I | S | R | D | T | S | K | S | Q | G | F | L | K | M | N | S | L | Q | T | D | D | T | A | I | Y | F | C | T | S | N | R | E | S | Y | Y | F | D | Y | W | G | Q | G | T | M | 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 | 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 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | I | K | M | T | Q | S | P | A | S | L | S | A | S | L | G | D | K | V | T | I | T | C | Q | A | S | Q | N | I | D | K | Y | I | A | W | Y | Q | Q | K | P | G | K | A | P | R | Q | L | I | H | Y | T | S | T | L | V | S | G | T | P | S | R | F | S | G | S | G | S | G | R | D | Y | T | F | S | I | S | S | V | E | S | E | D | I | A | S | Y | Y | C | L | Q | Y | D | T | L | Y | T | F | G | A | G | T | K | L | E | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | F |
| Antigen type | protein |
| Antigen name | t-cell surface glycoprotein cd8 beta chain |
| Antigen species | MUS MUSCULUS |
| Antigen sequence | LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDVSSADLVPR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSLISD |
| CDRH2 | WADGS |
| CDRH3 | NRESYYFDY |
| CDRL1 | QASQNIDKYIA |
| CDRL2 | YTSTLVS |
| CDRL3 | LQYDTLYT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -56.8° |
| HC1 | 73.37° |
| HC2 | 121.53° |
| LC1 | 121.82° |
| LC2 | 78.29° |
| dc | 16.12Å |
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]
