Crystal Structure of the Igg2a Lpt3 in complex with an 8-Sugar inner Core analogue of Neisseria Meningitidis
| PDB | 4c83 |
| Species | MUS MUSCULUS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.69Å |
| 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 | A |
| Light chain | B |
| Heavy subgroup | IGHV5 |
| Light subgroup | IGKV4 |
| Species | MUS MUSCULUS |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | V | Q | L | V | E | S | G | G | G | L | V | Q | P | G | G | S | R | K | L | S | C | A | A | S | G | F | T | F | R | R | F | G | M | H | W | V | R | Q | S | P | E | K | G | L | E | W | V | A | Y | I | G | G | G | S | S | T | I | Y | Y | A | D | T | V | K | G | R | F | T | I | S | R | D | N | P | K | N | T | L | F | L | Q | M | T | S | L | R | S | E | D | T | A | M | Y | Y | C | T | R | D | E | T | G | S | W | F | A | Y | W | G | Q | G | T | L | V | T | V | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | I | V | L | S | Q | S | P | A | I | M | S | A | S | P | G | E | K | V | T | M | T | C | S | A | S | S | S | V | R | Y | M | H | W | Y | Q | Q | K | S | G | T | S | P | K | R | W | I | Y | D | T | S | K | L | A | S | G | V | P | T | R | F | S | G | S | G | S | G | T | S | Y | S | L | P | I | S | S | M | E | A | E | D | G | A | S | Y | Y | C | Q | Q | W | N | G | Y | P | P | L | T | F | G | G | G | T | K | L | E | M | K |
| Antigen Details | |
|---|---|
| Antigen chains | A |
| Antigen type | carbohydrate |
| Antigen name | polysaccharide |
| Antigen species | MUS MUSCULUS |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFTFRRF |
| CDRH2 | GGGSST |
| CDRH3 | DETGSWFAY |
| CDRL1 | SASSSVRYMH |
| CDRL2 | DTSKLAS |
| CDRL3 | QQWNGYPPLT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -58.25° |
| HC1 | 73.96° |
| HC2 | 118.5° |
| LC1 | 116.13° |
| LC2 | 82.54° |
| dc | 16.38Å |
| Fv Details | |
|---|---|
| Heavy chain | C |
| Light chain | D |
| Heavy subgroup | IGHV5 |
| Light subgroup | IGKV4 |
| Species | MUS MUSCULUS |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | V | Q | L | V | E | S | G | G | G | L | V | Q | P | G | G | S | R | K | L | S | C | A | A | S | G | F | T | F | R | R | F | G | M | H | W | V | R | Q | S | P | E | K | G | L | E | W | V | A | Y | I | G | G | G | S | S | T | I | Y | Y | A | D | T | V | K | G | R | F | T | I | S | R | D | N | P | K | N | T | L | F | L | Q | M | T | S | L | R | S | E | D | T | A | M | Y | Y | C | T | R | D | E | T | G | S | W | F | A | Y | W | G | Q | G | T | L | V | T | V | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | I | V | L | S | Q | S | P | A | I | M | S | A | S | P | G | E | K | V | T | M | T | C | S | A | S | S | S | V | R | Y | M | H | W | Y | Q | Q | K | S | G | T | S | P | K | R | W | I | Y | D | T | S | K | L | A | S | G | V | P | T | R | F | S | G | S | G | S | G | T | S | Y | S | L | P | I | S | S | M | E | A | E | D | G | A | S | Y | Y | C | Q | Q | W | N | G | Y | P | P | L | T | F | G | G | G | T | K | L | E | M | K |
| Antigen Details | |
|---|---|
| Antigen chains | C |
| Antigen type | carbohydrate |
| Antigen name | polysaccharide |
| Antigen species | MUS MUSCULUS |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFTFRRF |
| CDRH2 | GGGSST |
| CDRH3 | DETGSWFAY |
| CDRL1 | SASSSVRYMH |
| CDRL2 | DTSKLAS |
| CDRL3 | QQWNGYPPLT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -57.48° |
| HC1 | 74.25° |
| HC2 | 118.19° |
| LC1 | 115.85° |
| LC2 | 82.83° |
| dc | 16.27Å |
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]
