Crystal Structure of a Stabilized Ds-Sosip.6Mut Bg505 Gp140 Hiv-1 Env Trimer, Containing Mutations I201C-P433C (Ds), L154M, Y177W, N300M, N302M, T320L, I420M in complex with Human antibodies Pgt122 and 35O22 at 4.3 a
| PDB | 5utf |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 3.503Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Lambda,unknown |
| Has constant region | True |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | D |
| Light chain | E |
| Heavy subgroup | unknown |
| Light subgroup | unknown |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | True |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 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 | 73A | 73B | 73C | 73D | 73E | 73F | 73G | 73H | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | L | V | Q | S | G | A | E | L | K | K | P | G | A | S | V | K | I | S | C | K | T | S | G | Y | R | F | N | F | Y | H | I | N | W | I | R | Q | T | A | G | R | G | P | E | W | M | G | W | I | S | P | Y | S | G | D | K | N | L | A | P | A | F | Q | D | R | V | I | M | T | T | D | T | E | V | P | V | T | S | F | T | S | T | G | A | A | Y | M | E | I | R | N | L | K | F | D | D | T | G | T | Y | F | C | A | K | G | L | L | R | D | G | S | S | T | W | L | P | Y | L | W | G | Q | G | T | L | L | 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 | 30C | 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 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | S | V | L | T | Q | S | A | S | V | S | G | S | L | G | Q | S | V | T | I | S | C | T | G | P | N | S | V | C | C | S | H | K | S | I | S | W | Y | Q | W | P | P | G | R | A | P | T | L | I | I | Y | E | D | N | E | R | A | P | G | I | S | P | R | F | S | G | Y | K | S | Y | W | S | A | Y | L | T | I | S | D | L | R | P | E | D | E | T | T | Y | Y | C | C | S | Y | T | H | N | S | G | C | V | F | G | T | G | T | K | V | S | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | B |
| Antigen type | protein |
| Antigen name | envelope glycoprotein gp41 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GYRFNFY |
| CDRH2 | SPYSGD |
| CDRH3 | GLLRDGSSTWLPYL |
| CDRL1 | TGPNSVCCSHKSIS |
| CDRL2 | EDNERAP |
| CDRL3 | CSYTHNSGCV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -60.51° |
| HC1 | 73.07° |
| HC2 | 120.9° |
| LC1 | 118.37° |
| LC2 | 86.8° |
| dc | 16.37Å |
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV4 |
| Light subgroup | IGLV3 |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | H | L | Q | E | S | G | P | G | L | V | K | P | S | E | T | L | S | L | T | C | N | V | S | G | T | L | V | R | D | N | Y | W | S | W | I | R | Q | P | L | G | K | Q | P | E | W | I | G | Y | V | H | D | S | G | D | T | N | Y | N | P | S | L | K | S | R | V | H | L | S | L | D | K | S | K | N | L | V | S | L | R | L | T | G | V | T | A | A | D | S | A | I | Y | Y | C | A | T | T | K | H | G | R | R | I | Y | G | V | V | A | F | K | E | W | F | T | Y | F | Y | M | D | V | W | G | K | G | T | S | V | T | V | S | S |
Light chain
| 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 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 66A | 66B | 66C | 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 | 95C | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P | T | F | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | E | E | S | L | G | S | R | S | V | I | W | Y | Q | Q | R | P | G | Q | A | P | S | L | I | I | Y | N | N | N | D | R | P | S | G | I | P | D | R | F | S | G | S | P | G | S | T | F | G | T | T | A | T | L | T | I | T | S | V | E | A | G | D | E | A | D | Y | Y | C | H | I | W | D | S | R | R | P | T | N | W | V | F | G | E | G | T | T | L | I | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | G |
| Antigen type | protein |
| Antigen name | envelope glycoprotein gp120 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGEMKNCSFNMTTELRDKKQKVYSLFWRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPMNMTRKSIRIGPGQAFYALGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRMKQIINMWQRIGQCMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GTLVRDN |
| CDRH2 | HDSGD |
| CDRH3 | TKHGRRIYGVVAFKEWFTYFYMDV |
| CDRL1 | GEESLGSRSVI |
| CDRL2 | NNNDRPS |
| CDRL3 | HIWDSRRPTNWV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -64.01° |
| HC1 | 74.94° |
| HC2 | 123.1° |
| LC1 | 117.0° |
| LC2 | 86.09° |
| dc | 16.32Å |
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]
