Crystal Structure of Vh1-46 Germline-Derived Cd4-Binding Site-Directed antibody 1B2530 in complex with Hiv-1 Clade a/E 93Th057 Gp120
| PDB | 4yfl |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 3.387Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Lambda |
| 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 | unknown |
| Light subgroup | IGLV1 |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | Q | L | E | Q | S | G | T | A | V | R | K | P | G | A | S | V | T | L | S | C | Q | A | S | G | Y | N | F | V | K | Y | I | I | H | W | V | R | Q | K | P | G | L | G | F | E | W | V | G | M | I | D | P | Y | R | G | R | P | W | S | A | H | K | F | Q | G | R | L | S | L | S | R | D | T | S | M | E | I | L | Y | M | T | L | T | S | L | K | S | D | D | T | A | T | Y | F | C | A | R | A | E | A | A | S | D | S | H | S | R | P | I | M | F | D | H | W | G | Q | G | S | L | 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 | 30A | 30B | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | S | A | L | T | Q | P | P | S | A | S | G | A | P | G | Q | R | V | T | I | S | C | S | G | G | P | S | N | V | G | G | N | Y | V | Y | W | Y | R | Q | F | P | G | T | A | P | T | L | L | I | L | R | D | D | Q | R | P | S | G | V | P | D | R | F | S | A | S | K | S | G | N | S | A | S | L | A | I | S | G | L | R | P | D | D | E | G | F | Y | F | C | A | T | Y | D | S | D | G | S | I | R | L | F | G | G | G | T | A | L | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | G |
| Antigen type | protein |
| Antigen name | envelope glycoprotein gp160,envelope glycoprotein gp160,envelope glycoprotein gp160 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYNFVKY |
| CDRH2 | DPYRGR |
| CDRH3 | AEAASDSHSRPIMFDH |
| CDRL1 | SGGPSNVGGNYVY |
| CDRL2 | RDDQRPS |
| CDRL3 | ATYDSDGSIRL |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -56.79° |
| HC1 | 73.75° |
| HC2 | 109.78° |
| LC1 | 122.71° |
| LC2 | 79.59° |
| dc | 16.13Å |
| Fv Details | |
|---|---|
| Heavy chain | F |
| Light chain | I |
| Heavy subgroup | unknown |
| Light subgroup | IGLV1 |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | Q | L | E | Q | S | G | T | A | V | R | K | P | G | A | S | V | T | L | S | C | Q | A | S | G | Y | N | F | V | K | Y | I | I | H | W | V | R | Q | K | P | G | L | G | F | E | W | V | G | M | I | D | P | Y | R | G | R | P | W | S | A | H | K | F | Q | G | R | L | S | L | S | R | D | T | S | M | E | I | L | Y | M | T | L | T | S | L | K | S | D | D | T | A | T | Y | F | C | A | R | A | E | A | A | S | D | S | H | S | R | P | I | M | F | D | H | W | G | Q | G | S | L | 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 | 30A | 30B | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | S | A | L | T | Q | P | P | S | A | S | G | A | P | G | Q | R | V | T | I | S | C | S | G | G | P | S | N | V | G | G | N | Y | V | Y | W | Y | R | Q | F | P | G | T | A | P | T | L | L | I | L | R | D | D | Q | R | P | S | G | V | P | D | R | F | S | A | S | K | S | G | N | S | A | S | L | A | I | S | G | L | R | P | D | D | E | G | F | Y | F | C | A | T | Y | D | S | D | G | S | I | R | L | F | G | G | G | T | A | L | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | E |
| Antigen type | protein |
| Antigen name | envelope glycoprotein gp160,envelope glycoprotein gp160,envelope glycoprotein gp160 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYNFVKY |
| CDRH2 | DPYRGR |
| CDRH3 | AEAASDSHSRPIMFDH |
| CDRL1 | SGGPSNVGGNYVY |
| CDRL2 | RDDQRPS |
| CDRL3 | ATYDSDGSIRL |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -64.48° |
| HC1 | 71.36° |
| HC2 | 106.92° |
| LC1 | 120.95° |
| LC2 | 73.6° |
| dc | 15.85Å |
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]
