Crystal Structure of the Outer Domain of Hiv-1 Gp120 in complex with Vrc-Pg04 Space Group P3221
| PDB | 4i3r |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 3.0Å |
| Number of Fvs | 1 |
| In complex | True |
| Light chain type | unknown |
| 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 | unknown |
| Light subgroup | unknown |
| 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 | 31A | 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 | 59A | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q | V | Q | L | V | Q | S | G | S | G | V | K | K | P | G | A | S | V | R | V | S | C | W | T | S | E | D | I | F | E | R | T | E | L | I | H | W | V | R | Q | A | P | G | Q | G | L | E | W | I | G | W | V | K | T | V | T | G | A | V | N | F | G | S | P | D | F | R | Q | R | V | S | L | T | R | D | R | D | L | F | T | A | H | M | D | I | R | G | L | T | Q | G | D | T | A | T | Y | F | C | A | R | Q | K | F | Y | T | G | G | Q | G | W | Y | F | D | L | W | G | R | G | T | L | I | V | 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 | 26 | 27 | 28 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E | I | V | L | T | Q | S | P | G | T | L | S | L | S | P | G | E | T | A | S | L | S | C | T | A | A | S | Y | G | H | M | T | W | Y | Q | K | K | P | G | Q | P | P | K | L | L | I | F | A | T | S | K | R | A | S | G | I | P | D | R | F | S | G | S | Q | F | G | K | Q | Y | T | L | T | I | T | R | M | E | P | E | D | F | A | R | Y | Y | C | Q | Q | L | E | F | F | G | Q | G | T | R | L | E | I | R |
| Antigen Details | |
|---|---|
| Antigen chains | G |
| Antigen type | protein |
| Antigen name | outer domain of hiv-1 gp120 (ker2018 od4.2.2) |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS |
| Antigen sequence | KPVVSTQLLLNGSLAEKEIRIKSEDISDNAKNIIVQLTKPVLINCARPSNNTQYCVVNRTQWNDTLGQVAIQLRKHWNTCIIFNEPSGGDLEITTHSFNCGGEFFYCNTSDLFNSTWNIEGTASIDGTESNDDITLPCRIKGSGAPPIQGVIRCQSNITGILLTRDGGSGSGTCETFRPGGGDMRDNWRS |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | EDIFERTE |
| CDRH2 | KTVTGA |
| CDRH3 | QKFYTGGQGWYFDL |
| CDRL1 | TAASYGHMT |
| CDRL2 | ATSKRAS |
| CDRL3 | QQLEF |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -56.52° |
| HC1 | 71.32° |
| HC2 | 115.81° |
| LC1 | 121.64° |
| LC2 | 84.79° |
| dc | 16.31Å |
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]
