Crystal Structure of Human Fab Pgt144, a Broadly Reactive and Potent Hiv-1 Neutralizing antibody
| PDB | 5uy3 |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.9Å |
| 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 | unknown |
| Light subgroup | IGKV2 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 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 | 100D | 100E | 100F | 100G | 100H | 100I | 100J | 100K | 100L | 100M | 100N | 100O | 100P | 100Q | 100R | 100S | 100T | 100U | 100V | 100W | 100X | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| L | V | Q | S | G | A | E | V | K | K | P | G | S | S | V | K | V | S | C | K | A | S | G | N | T | F | R | K | Y | D | V | H | W | V | R | Q | A | T | G | Q | G | L | E | W | V | G | W | M | S | H | E | G | D | K | T | E | S | A | Q | R | F | K | G | R | V | S | F | T | R | D | N | S | A | S | T | A | Y | I | E | L | R | G | L | T | S | D | D | T | A | I | Y | Y | C | T | G | G | S | K | H | R | L | R | D | Y | V | L | Y | D | D | Y | G | L | I | N | Q | Q | E | W | N | D | Y | L | E | F | L | D | V | W | G | H | G | T | A | V | T | V | S | S |
Light 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 | 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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| T | V | V | T | Q | S | P | L | S | L | S | V | T | P | G | E | A | A | S | M | S | C | T | S | T | Q | S | L | R | H | S | N | G | A | N | Y | L | A | W | Y | Q | H | K | P | G | Q | S | P | R | L | L | I | R | L | G | S | Q | R | A | S | G | V | P | D | R | F | S | G | S | G | S | G | T | H | F | T | L | K | I | S | R | V | E | A | D | D | A | A | I | Y | Y | C | M | Q | G | L | N | R | P | W | T | F | G | K | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | |
| Antigen type | |
| Antigen name | |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GNTFRKY |
| CDRH2 | SHEGDK |
| CDRH3 | GSKHRLRDYVLYDDYGLINQQEWNDYLEFLDV |
| CDRL1 | TSTQSLRHSNGANYLA |
| CDRL2 | LGSQRAS |
| CDRL3 | MQGLNRPWT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -55.52° |
| HC1 | 73.22° |
| HC2 | 123.18° |
| LC1 | 122.98° |
| LC2 | 83.58° |
| dc | 16.31Å |
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | unknown |
| Light subgroup | IGKV2 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 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 | 100D | 100E | 100F | 100G | 100H | 100I | 100J | 100K | 100L | 100M | 100N | 100O | 100P | 100Q | 100R | 100S | 100T | 100U | 100V | 100W | 100X | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| L | V | Q | S | G | A | E | V | K | K | P | G | S | S | V | K | V | S | C | K | A | S | G | N | T | F | R | K | Y | D | V | H | W | V | R | Q | A | T | G | Q | G | L | E | W | V | G | W | M | S | H | E | G | D | K | T | E | S | A | Q | R | F | K | G | R | V | S | F | T | R | D | N | S | A | S | T | A | Y | I | E | L | R | G | L | T | S | D | D | T | A | I | Y | Y | C | T | G | G | S | K | H | R | L | R | D | Y | V | L | Y | D | D | Y | G | L | I | N | Q | Q | E | W | N | D | Y | L | E | F | L | D | V | W | G | H | G | T | A | V | T | V | S | S |
Light 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 | 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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| T | V | V | T | Q | S | P | L | S | L | S | V | T | P | G | E | A | A | S | M | S | C | T | S | T | Q | S | L | R | H | S | N | G | A | N | Y | L | A | W | Y | Q | H | K | P | G | Q | S | P | R | L | L | I | R | L | G | S | Q | R | A | S | G | V | P | D | R | F | S | G | S | G | S | G | T | H | F | T | L | K | I | S | R | V | E | A | D | D | A | A | I | Y | Y | C | M | Q | G | L | N | R | P | W | T | F | G | K | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | |
| Antigen type | |
| Antigen name | |
| Antigen species | SYNTHETIC CONSTRUCT |
| Antigen sequence | |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GNTFRKY |
| CDRH2 | SHEGDK |
| CDRH3 | GSKHRLRDYVLYDDYGLINQQEWNDYLEFLDV |
| CDRL1 | TSTQSLRHSNGANYLA |
| CDRL2 | LGSQRAS |
| CDRL3 | MQGLNRPWT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -55.6° |
| HC1 | 71.98° |
| HC2 | 121.44° |
| LC1 | 124.27° |
| LC2 | 84.82° |
| dc | 16.11Å |
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]
