Crystal Structure of Fab From 3Bnc60, Highly Potent anti-Hiv antibody
| PDB | 3rpi |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.648Å |
| 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 | IGHV1 |
| 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 | 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 | 76A | 76B | 76C | 76D | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | V | H | L | S | Q | S | G | A | A | V | T | K | P | G | A | S | V | R | V | S | C | E | A | S | G | Y | K | I | S | D | H | F | I | H | W | W | R | Q | A | P | G | Q | G | L | Q | W | V | G | W | I | N | P | K | T | G | Q | P | N | N | P | R | Q | F | Q | G | R | V | S | L | T | R | Q | A | S | W | D | F | D | T | Y | S | F | Y | M | D | L | K | A | V | R | S | D | D | T | A | I | Y | F | C | A | R | Q | R | S | D | F | W | D | F | D | V | W | G | S | G | T | Q | 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 | 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 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | I | Q | M | T | Q | S | P | S | S | L | S | A | R | V | G | D | T | V | T | I | T | C | Q | A | N | G | Y | L | N | W | Y | Q | Q | R | R | G | K | A | P | K | L | L | I | Y | D | G | S | K | L | E | R | G | V | P | A | R | F | S | G | R | R | W | G | Q | E | Y | N | L | T | I | N | N | L | Q | P | E | D | V | A | T | Y | F | C | Q | V | Y | E | F | I | V | P | G | T | R | L | D | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | |
| Antigen type | |
| Antigen name | |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYKISDH |
| CDRH2 | NPKTGQ |
| CDRH3 | QRSDFWDFDV |
| CDRL1 | QANGYLN |
| CDRL2 | DGSKLER |
| CDRL3 | QVYEF |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -59.28° |
| HC1 | 72.65° |
| HC2 | 111.88° |
| LC1 | 122.7° |
| LC2 | 84.14° |
| dc | 16.67Å |
| Fv Details | |
|---|---|
| Heavy chain | A |
| Light chain | B |
| Heavy subgroup | IGHV1 |
| 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 | 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 | 76A | 76B | 76C | 76D | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | H | L | S | Q | S | G | A | A | V | T | K | P | G | A | S | V | R | V | S | C | E | A | S | G | Y | K | I | S | D | H | F | I | H | W | W | R | Q | A | P | G | Q | G | L | Q | W | V | G | W | I | N | P | K | T | G | Q | P | N | N | P | R | Q | F | Q | G | R | V | S | L | T | R | Q | A | S | W | D | F | D | T | Y | S | F | Y | M | D | L | K | A | V | R | S | D | D | T | A | I | Y | F | C | A | R | Q | R | S | D | F | W | D | F | D | V | W | G | S | G | T | Q | 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 | 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 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | I | Q | M | T | Q | S | P | S | S | L | S | A | R | V | G | D | T | V | T | I | T | C | Q | A | N | G | Y | L | N | W | Y | Q | Q | R | R | G | K | A | P | K | L | L | I | Y | D | G | S | K | L | E | R | G | V | P | A | R | F | S | G | R | R | W | G | Q | E | Y | N | L | T | I | N | N | L | Q | P | E | D | V | A | T | Y | F | C | Q | V | Y | E | F | I | V | P | G | T | R | L | D | L | K |
| Antigen Details | |
|---|---|
| Antigen chains | |
| Antigen type | |
| Antigen name | |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYKISDH |
| CDRH2 | NPKTGQ |
| CDRH3 | QRSDFWDFDV |
| CDRL1 | QANGYLN |
| CDRL2 | DGSKLER |
| CDRL3 | QVYEF |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -59.66° |
| HC1 | 72.07° |
| HC2 | 111.4° |
| LC1 | 122.88° |
| LC2 | 84.25° |
| dc | 16.71Å |
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]
