Crystal Structure of the Fab Fragment of the Human Hiv-1 Neutralizing antibody Pgzl1.H4K3 in complex with Its Mper Peptide Epitope (Region 671-683 of Hiv-1 Gp41).
| PDB | 6o3l |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 1.98Å |
| 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 | IGHV1 |
| Light subgroup | IGKV3 |
| 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| K | V | Q | L | V | Q | S | G | A | E | L | K | K | P | W | S | S | V | R | V | S | C | K | A | S | G | G | S | F | S | S | Y | A | F | N | W | V | R | Q | A | P | G | Q | R | L | E | W | L | G | G | I | V | P | L | V | S | S | T | N | Y | A | Q | R | F | R | G | R | V | T | I | S | A | D | R | S | T | S | T | V | Y | L | E | M | T | G | L | T | S | A | D | T | A | V | Y | F | C | A | R | E | G | E | G | W | F | G | R | P | L | R | A | F | E | F | W | G | Q | G | T | L | V | T | V | S | T |
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 | 29 | 30 | 30A | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E | I | V | L | T | Q | S | P | G | T | F | A | L | S | P | G | E | R | A | T | L | S | C | R | A | S | Q | S | V | S | G | G | A | L | A | W | Y | Q | Q | K | A | G | Q | A | P | R | L | L | I | Y | G | T | S | G | R | A | T | G | V | P | G | R | F | S | G | S | G | S | E | T | D | F | S | L | T | I | S | R | L | E | P | E | D | F | A | V | Y | Y | C | Q | Q | Y | G | T | S | Q | S | T | F | G | Q | G | T | R | L | E | T | R |
| Antigen Details | |
|---|---|
| Antigen chains | E |
| Antigen type | peptide |
| Antigen name | mper peptide, region 671-683 of hiv-1 gp41 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | NWFDITNWLWYIKKKK |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GGSFSSY |
| CDRH2 | VPLVSS |
| CDRH3 | EGEGWFGRPLRAFEF |
| CDRL1 | RASQSVSGGALA |
| CDRL2 | GTSGRAT |
| CDRL3 | QQYGTSQST |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -59.5° |
| HC1 | 70.15° |
| HC2 | 119.76° |
| LC1 | 119.78° |
| LC2 | 83.52° |
| dc | 16.01Å |
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV1 |
| Light subgroup | IGKV3 |
| 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| K | V | Q | L | V | Q | S | G | A | E | L | K | K | P | W | S | S | V | R | V | S | C | K | A | S | G | G | S | F | S | S | Y | A | F | N | W | V | R | Q | A | P | G | Q | R | L | E | W | L | G | G | I | V | P | L | V | S | S | T | N | Y | A | Q | R | F | R | G | R | V | T | I | S | A | D | R | S | T | S | T | V | Y | L | E | M | T | G | L | T | S | A | D | T | A | V | Y | F | C | A | R | E | G | E | G | W | F | G | R | P | L | R | A | F | E | F | W | G | Q | G | T | L | V | T | V | S | T |
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 | 29 | 30 | 30A | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E | I | V | L | T | Q | S | P | G | T | F | A | L | S | P | G | E | R | A | T | L | S | C | R | A | S | Q | S | V | S | G | G | A | L | A | W | Y | Q | Q | K | A | G | Q | A | P | R | L | L | I | Y | G | T | S | G | R | A | T | G | V | P | G | R | F | S | G | S | G | S | E | T | D | F | S | L | T | I | S | R | L | E | P | E | D | F | A | V | Y | Y | C | Q | Q | Y | G | T | S | Q | S | T | F | G | Q | G | T | R | L | E | T | R |
| Antigen Details | |
|---|---|
| Antigen chains | D |
| Antigen type | peptide |
| Antigen name | mper peptide, region 671-683 of hiv-1 gp41 |
| Antigen species | HUMAN IMMUNODEFICIENCY VIRUS 1 |
| Antigen sequence | NWFDITNWLWYIKKKK |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GGSFSSY |
| CDRH2 | VPLVSS |
| CDRH3 | EGEGWFGRPLRAFEF |
| CDRL1 | RASQSVSGGALA |
| CDRL2 | GTSGRAT |
| CDRL3 | QQYGTSQST |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -57.26° |
| HC1 | 69.81° |
| HC2 | 119.33° |
| LC1 | 119.23° |
| LC2 | 85.15° |
| dc | 16.1Å |
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]
