Crystal Structure of Vascular Endothelial Growth Factor-B in complex with a Neutralizing antibody Fab Fragment
PDB | 2vwe |
Species | MUS MUSCULUS |
Method | X-RAY DIFFRACTION |
Resolution | 3.4Å |
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 | E |
Light chain | C |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV10 |
Species | MUS MUSCULUS |
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 | 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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Q | V | Q | L | Q | Q | P | G | T | E | L | V | K | P | G | A | S | V | K | L | S | C | K | A | S | G | Y | T | F | T | G | F | W | I | H | W | V | K | Q | R | P | G | Q | G | L | E | W | I | G | H | I | N | P | G | N | G | G | T | N | Y | N | E | K | F | K | R | M | A | T | L | T | V | D | K | S | S | S | T | A | Y | M | Q | L | S | S | L | T | S | E | D | S | A | V | Y | Y | C | A | R | S | Y | S | N | Y | V | R | A | M | D | Y | 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 |
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E | I | Q | M | T | Q | T | T | S | S | L | S | A | S | L | G | D | R | V | T | I | S | C | R | A | S | Q | D | I | S | N | F | L | N | W | Y | Q | Q | K | P | D | G | T | V | K | L | L | I | Y | Y | T | S | T | L | H | S | G | V | P | S | R | F | S | G | S | G | S | G | T | D | Y | S | L | T | I | S | N | L | E | Q | E | D | I | A | T | Y | F | C | Q | Q | G | K | T | L | P | P | T | F | G | G | G | T | K | L | E | I | K |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | vascular endothelial growth factor b |
Antigen species | HOMO SAPIENS |
Antigen sequence | PVSQPDAPGHQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKKDSAVKPDSPRPLCPRCTQHHQRPDPRTCRCRCRRRSFLRCQGRGLELNPDTCRCRKLRR |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYTFTGF |
CDRH2 | NPGNGG |
CDRH3 | SYSNYVRAMDY |
CDRL1 | RASQDISNFLN |
CDRL2 | YTSTLHS |
CDRL3 | QQGKTLPPT |
Orientation Angles (from ABangle) | |
---|---|
HL | -60.21° |
HC1 | 69.49° |
HC2 | 111.41° |
LC1 | 120.07° |
LC2 | 81.37° |
dc | 16.22Å |
Fv Details | |
---|---|
Heavy chain | L |
Light chain | J |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV10 |
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 | 100B | 100C | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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Q | V | Q | L | Q | Q | P | G | T | E | L | V | K | P | G | A | S | V | K | L | S | C | K | A | S | G | Y | T | F | T | G | F | W | I | H | W | V | K | Q | R | P | G | Q | G | L | E | W | I | G | H | I | N | P | G | N | G | G | T | N | Y | N | E | K | F | K | R | M | A | T | L | T | V | D | K | S | S | S | T | A | Y | M | Q | L | S | S | L | T | S | E | D | S | A | V | Y | Y | C | A | R | S | Y | S | N | Y | V | R | A | M | D | Y | 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 |
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E | I | Q | M | T | Q | T | T | S | S | L | S | A | S | L | G | D | R | V | T | I | S | C | R | A | S | Q | D | I | S | N | F | L | N | W | Y | Q | Q | K | P | D | G | T | V | K | L | L | I | Y | Y | T | S | T | L | H | S | G | V | P | S | R | F | S | G | S | G | S | G | T | D | Y | S | L | T | I | S | N | L | E | Q | E | D | I | A | T | Y | F | C | Q | Q | G | K | T | L | P | P | T | F | G | G | G | T | K | L | E | I | K |
Antigen Details | |
---|---|
Antigen chains | B |
Antigen type | protein |
Antigen name | vascular endothelial growth factor b |
Antigen species | HOMO SAPIENS |
Antigen sequence | PVSQPDAPGHQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKKDSAVKPDSPRPLCPRCTQHHQRPDPRTCRCRCRRRSFLRCQGRGLELNPDTCRCRKLRR |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYTFTGF |
CDRH2 | NPGNGG |
CDRH3 | SYSNYVRAMDY |
CDRL1 | RASQDISNFLN |
CDRL2 | YTSTLHS |
CDRL3 | QQGKTLPPT |
Orientation Angles (from ABangle) | |
---|---|
HL | -60.5° |
HC1 | 69.25° |
HC2 | 111.98° |
LC1 | 120.78° |
LC2 | 80.66° |
dc | 16.32Å |
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]