Crystal Structure of anti-Ige antibody Hmk-12 Fab complexed with Ige F(ab')2
| PDB | 8xx0 |
| Species | RATTUS; MUS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.9Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | unknown,Kappa |
| Has constant region | True |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV3 |
| Light subgroup | IGKV16 |
| Species | 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 | 31A | 31B | 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 | 82A | 82B | 82C | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 100A | 100B | 100C | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| D | V | Q | L | Q | E | S | G | P | G | F | V | T | P | S | Q | S | L | S | V | T | C | S | V | T | G | Y | S | L | T | A | S | S | Y | F | W | N | W | I | R | K | F | P | G | N | K | L | E | W | M | G | Y | I | G | Y | D | G | S | V | Y | Y | N | P | S | L | K | S | R | I | S | I | T | R | D | T | S | K | R | Q | F | F | L | Q | L | K | T | V | T | N | D | D | T | A | L | Y | Y | C | A | R | H | G | Y | Y | S | S | R | V | M | D | A | W | G | Q | G | T | S | 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 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | V | Q | M | N | Q | S | P | S | N | L | A | A | S | P | G | E | T | V | S | I | N | C | K | A | S | K | S | I | S | R | Y | L | A | W | Y | Q | Q | K | P | G | K | A | N | K | L | L | I | F | S | G | S | T | L | Q | S | G | T | P | S | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | R | N | L | E | P | E | D | F | G | L | Y | F | C | Q | Q | H | N | E | F | P | L | T | F | G | S | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | H |
| Antigen type | carbohydrate |
| Antigen name | B-OCTYLGLUCOSIDE |
| Antigen species | RATTUS |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYSLTASSY |
| CDRH2 | GYDGS |
| CDRH3 | HGYYSSRVMDA |
| CDRL1 | KASKSISRYLA |
| CDRL2 | SGSTLQS |
| CDRL3 | QQHNEFPLT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -73.31° |
| HC1 | 72.91° |
| HC2 | 112.71° |
| LC1 | 114.6° |
| LC2 | 74.32° |
| dc | 16.21Å |
| Fv Details | |
|---|---|
| Heavy chain | A |
| Light chain | B |
| Heavy subgroup | IGHV1 |
| Light subgroup | unknown |
| Species | MUS |
| In complex? | False |
| 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 | 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 | 100C | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| E | V | Q | L | Q | Q | P | G | A | E | L | V | K | P | G | A | S | V | K | L | S | C | K | A | S | G | Y | T | F | T | S | Y | W | M | H | W | V | K | Q | R | P | G | R | G | L | E | W | I | G | R | I | D | P | N | G | G | G | T | K | Y | N | E | K | F | K | S | K | A | T | L | T | V | D | K | P | S | S | T | A | Y | M | Q | L | S | S | L | T | S | E | D | S | A | V | Y | Y | C | A | R | M | W | Y | Y | G | T | Y | Y | 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 | 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 | 54 | 55 | 56 | 57 | 58 | 59 | 59A | 60 | 62 | 63 | 64 | 65 | 66 | 66A | 66B | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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| Q | A | V | V | T | Q | E | S | A | L | T | T | S | P | G | E | T | V | T | L | T | C | R | S | S | T | G | A | V | T | T | S | N | Y | A | N | W | V | Q | E | K | P | D | H | L | F | T | G | L | I | G | G | T | N | N | R | A | P | G | V | P | A | R | F | S | G | S | L | I | G | D | K | A | A | L | T | I | T | G | A | Q | T | E | D | E | A | I | Y | F | C | A | L | W | Y | S | N | H | L | V | F | G | G | G | T | K | L | T | V | L |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYTFTSY |
| CDRH2 | DPNGGG |
| CDRH3 | MWYYGTYYFDY |
| CDRL1 | RSSTGAVTTSNYAN |
| CDRL2 | GTNNR |
| CDRL3 | FCALWYSNHLV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -64.53° |
| HC1 | 68.05° |
| HC2 | 112.88° |
| LC1 | 102.58° |
| LC2 | 83.96° |
| dc | 16.8Å |
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]
