Crystal Structure of Human Fab Cap256-Vrc26.25, a Potent V1V2-Directed Hiv-1 Broadly Neutralizing antibody
| PDB | 5dt1 |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 1.954Å |
| Number of Fvs | 1 |
| In complex | True |
| Light chain type | Lambda |
| Has constant region | True |
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Display options: |
This PDB has 1 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV3 |
| Light subgroup | IGLV1 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (imgt) |
|---|
Heavy chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 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 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 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 | 108 | 109 | 110 | 111 | 111A | 111B | 111C | 111D | 111E | 111F | 111G | 111H | 111I | 111J | 111K | 111L | 112 | 112A | 112B | 112C | 112D | 112E | 112F | 112G | 112H | 112I | 112J | 112K | 112L | 112M | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 |
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| Q | V | Q | L | V | E | S | G | G | G | V | V | Q | P | G | T | S | L | R | L | S | C | A | A | S | Q | F | R | F | D | G | Y | G | M | H | W | V | R | Q | A | P | G | K | G | L | E | W | V | A | S | I | S | H | D | G | I | K | K | Y | H | A | E | K | V | W | G | R | F | T | I | S | R | D | N | S | K | N | T | L | Y | L | Q | M | N | S | L | R | P | E | D | T | A | L | Y | Y | C | A | K | D | L | R | E | D | E | C | E | E | W | W | S | D | Y | Y | D | F | V | L | G | G | R | S | K | A | C | P | L | Q | K | G | G | I | A | D | N | W | G | Q | G | T | M | V | T | V | S | S |
Light chain
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 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 | 108 | 109 | 110 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 |
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| Q | S | V | L | T | Q | P | P | S | V | S | A | A | P | G | Q | K | V | T | I | S | C | S | G | N | T | S | N | I | G | N | N | F | V | S | W | Y | Q | Q | R | P | G | R | A | P | Q | L | L | I | Y | E | T | D | K | R | P | S | G | I | P | D | R | F | S | A | S | K | S | G | T | S | G | T | L | A | I | T | G | L | Q | T | G | D | E | A | D | Y | Y | C | A | T | W | A | A | S | L | S | S | A | R | V | F | G | T | G | T | K | V | I | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | L |
| Antigen type | carbohydrate |
| Antigen name | polysaccharide |
| Antigen species | HOMO SAPIENS |
| Antigen sequence | |
| CDR Sequences (imgt definition) | |
|---|---|
| CDRH1 | QFRFDGYG |
| CDRH2 | ISHDGIKK |
| CDRH3 | AKDLREDECEEWWSDYYDFGKQLPCAKSRGGLVGIADN |
| CDRL1 | TSNIGNNF |
| CDRL2 | ETD |
| CDRL3 | ATWAASLSSARV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -62.36° |
| HC1 | 70.65° |
| HC2 | 122.55° |
| LC1 | 117.96° |
| LC2 | 80.71° |
| dc | 15.92Å |
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]
