Crystal Structure of a Fab Fragment with the Ligand Peptide
PDB | 5aum |
Species | RATTUS |
Method | X-RAY DIFFRACTION |
Resolution | 2.05Å |
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 | A |
Light chain | B |
Heavy subgroup | IGHV10 |
Light subgroup | IGKV2 |
Species | RATTUS |
In complex? | True |
scFv? | False |
Has constant domain? | True |
Numbered Sequences (chothia) |
---|
Heavy chain
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 | 52B | 52C | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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V | Q | L | V | E | S | G | G | G | L | V | Q | P | K | E | S | L | K | I | S | C | A | A | F | G | V | T | F | S | N | V | A | M | Y | W | V | R | Q | A | P | G | K | G | L | E | W | V | A | R | I | R | T | K | P | N | N | Y | A | T | Y | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | D | S | K | S | M | V | Y | L | Q | M | D | N | L | K | T | E | D | T | A | M | Y | Y | C | T | A | E | V | A | T | D | W | G | Q | G | V | 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 | 30A | 30B | 30C | 30D | 30E | 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 | V | V | L | T | Q | A | P | P | T | L | S | A | T | I | G | Q | S | V | S | I | S | C | R | S | S | Q | S | L | L | H | R | N | G | N | T | Y | L | N | W | L | L | Q | R | P | G | Q | P | P | Q | L | L | I | Y | L | V | S | R | L | E | S | G | V | P | N | R | F | S | G | S | G | S | G | T | A | F | T | L | K | I | S | G | L | E | A | E | D | L | G | V | Y | Y | C | V | Q | G | T | H | A | P | L | T | F | G | S | G | T | K | L | E | I | K |
Antigen Details | |
---|---|
Antigen chains | D |
Antigen type | peptide |
Antigen name | peptide renlyfqgkdg |
Antigen species | POTYVIRIDAE |
Antigen sequence | RENLYFQGKDG |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GVTFSNV |
CDRH2 | RTKPNNYA |
CDRH3 | EVATD |
CDRL1 | RSSQSLLHRNGNTYLN |
CDRL2 | LVSRLES |
CDRL3 | VQGTHAPLT |
Orientation Angles (from ABangle) | |
---|---|
HL | -43.21° |
HC1 | 70.08° |
HC2 | 108.02° |
LC1 | 119.94° |
LC2 | 85.51° |
dc | 16.13Å |
Fv Details | |
---|---|
Heavy chain | H |
Light chain | L |
Heavy subgroup | IGHV10 |
Light subgroup | IGKV2 |
Species | RATTUS |
In complex? | True |
scFv? | False |
Has constant domain? | True |
Numbered Sequences (chothia) |
---|
Heavy chain
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 | 52B | 52C | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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V | Q | L | V | E | S | G | G | G | L | V | Q | P | K | E | S | L | K | I | S | C | A | A | F | G | V | T | F | S | N | V | A | M | Y | W | V | R | Q | A | P | G | K | G | L | E | W | V | A | R | I | R | T | K | P | N | N | Y | A | T | Y | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | D | S | K | S | M | V | Y | L | Q | M | D | N | L | K | T | E | D | T | A | M | Y | Y | C | T | A | E | V | A | T | D | W | G | Q | G | V | 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 | 30A | 30B | 30C | 30D | 30E | 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 | V | V | L | T | Q | A | P | P | T | L | S | A | T | I | G | Q | S | V | S | I | S | C | R | S | S | Q | S | L | L | H | R | N | G | N | T | Y | L | N | W | L | L | Q | R | P | G | Q | P | P | Q | L | L | I | Y | L | V | S | R | L | E | S | G | V | P | N | R | F | S | G | S | G | S | G | T | A | F | T | L | K | I | S | G | L | E | A | E | D | L | G | V | Y | Y | C | V | Q | G | T | H | A | P | L | T | F | G | S | G | T | K | L | E | I | K |
Antigen Details | |
---|---|
Antigen chains | C |
Antigen type | peptide |
Antigen name | peptide renlyfqgkdg |
Antigen species | POTYVIRIDAE |
Antigen sequence | RENLYFQGKDG |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GVTFSNV |
CDRH2 | RTKPNNYA |
CDRH3 | EVATD |
CDRL1 | RSSQSLLHRNGNTYLN |
CDRL2 | LVSRLES |
CDRL3 | VQGTHAPLT |
Orientation Angles (from ABangle) | |
---|---|
HL | -45.53° |
HC1 | 70.43° |
HC2 | 107.3° |
LC1 | 117.71° |
LC2 | 83.77° |
dc | 16.1Å |
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]