Structure of Omalizumab Fab Fragment, Crystal Form 2
PDB | 4x7t |
Species | HOMO SAPIENS |
Method | X-RAY DIFFRACTION |
Resolution | 3.0Å |
Number of Fvs | 2 |
In complex | True |
Light chain type | 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 | IGKV1 |
Species | HOMO SAPIENS |
In complex? | True |
scFv? | False |
Has constant domain? | True |
Numbered Sequences (chothia) |
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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 | 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 | 100B | 100C | 100D | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | V | E | S | G | G | G | L | V | Q | P | G | G | S | L | R | L | S | C | A | V | S | G | Y | S | I | T | S | G | Y | S | W | N | W | I | R | Q | A | P | G | K | G | L | E | W | V | A | S | I | T | Y | D | G | S | T | N | Y | N | P | S | V | K | G | R | I | T | I | S | R | D | D | S | K | N | T | F | Y | L | Q | M | N | S | L | R | A | E | D | T | A | V | Y | Y | C | A | R | G | S | H | Y | F | G | H | W | H | F | A | V | W | G | Q | G | T | L | 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 | 30A | 30B | 30C | 30D | 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 |
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D | I | Q | L | T | Q | S | P | S | S | L | S | A | S | V | G | D | R | V | T | I | T | C | R | A | S | Q | S | V | D | Y | D | G | D | S | Y | M | N | W | Y | Q | Q | K | P | G | K | A | P | K | L | L | I | Y | A | A | S | Y | L | E | S | G | V | P | S | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | S | S | L | Q | P | E | D | F | A | T | Y | Y | C | Q | Q | S | H | E | D | P | Y | T | F | G | Q | G | T | K | V | E | I | K |
Antigen Details | |
---|---|
Antigen chains | |
Antigen type | |
Antigen name | |
Antigen species | SYNTHETIC CONSTRUCT |
Antigen sequence |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYSITSGY |
CDRH2 | TYDGS |
CDRH3 | GSHYFGHWHFAV |
CDRL1 | RASQSVDYDGDSYMN |
CDRL2 | AASYLES |
CDRL3 | QQSHEDPYT |
Orientation Angles (from ABangle) | |
---|---|
HL | -61.79° |
HC1 | 73.8° |
HC2 | 118.19° |
LC1 | 118.97° |
LC2 | 82.54° |
dc | 16.09Å |
Fv Details | |
---|---|
Heavy chain | A |
Light chain | B |
Heavy subgroup | IGHV3 |
Light subgroup | IGKV1 |
Species | HOMO SAPIENS |
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 | 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 | 100B | 100C | 100D | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | V | E | S | G | G | G | L | V | Q | P | G | G | S | L | R | L | S | C | A | V | S | G | Y | S | I | T | S | G | Y | S | W | N | W | I | R | Q | A | P | G | K | G | L | E | W | V | A | S | I | T | Y | D | G | S | T | N | Y | N | P | S | V | K | G | R | I | T | I | S | R | D | D | S | K | N | T | F | Y | L | Q | M | N | S | L | R | A | E | D | T | A | V | Y | Y | C | A | R | G | S | H | Y | F | G | H | W | H | F | A | V | W | G | Q | G | T | L | 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 | 30A | 30B | 30C | 30D | 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 |
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D | I | Q | L | T | Q | S | P | S | S | L | S | A | S | V | G | D | R | V | T | I | T | C | R | A | S | Q | S | V | D | Y | D | G | D | S | Y | M | N | W | Y | Q | Q | K | P | G | K | A | P | K | L | L | I | Y | A | A | S | Y | L | E | S | G | V | P | S | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | S | S | L | Q | P | E | D | F | A | T | Y | Y | C | Q | Q | S | H | E | D | P | Y | T | F | G | Q | G | T | K | V | E | I | K |
Antigen Details | |
---|---|
Antigen chains | |
Antigen type | |
Antigen name | |
Antigen species | SYNTHETIC CONSTRUCT |
Antigen sequence |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYSITSGY |
CDRH2 | TYDGS |
CDRH3 | GSHYFGHWHFAV |
CDRL1 | RASQSVDYDGDSYMN |
CDRL2 | AASYLES |
CDRL3 | QQSHEDPYT |
Orientation Angles (from ABangle) | |
---|---|
HL | -60.65° |
HC1 | 74.03° |
HC2 | 119.46° |
LC1 | 119.07° |
LC2 | 82.0° |
dc | 16.16Å |
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]