Structure of Sars-Cov-2 Spike Protein Receptor Binding Domain in complex with a Neutralizing antibody, Cv2-75 Fab
| PDB | 7m3i |
| Species | HOMO SAPIENS |
| Method | X-RAY DIFFRACTION |
| Resolution | 2.8Å |
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | V | Q | L | Q | E | S | G | P | G | L | V | K | P | S | E | T | L | S | L | T | C | T | V | S | G | G | S | I | S | S | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | Y | V | Y | Y | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | V | D | T | S | K | N | E | F | S | L | K | L | S | S | V | T | A | A | D | T | A | V | Y | Y | C | A | S | S | Q | R | P | D | G | N | L | Y | Y | F | D | Y | W | G | Q | G | T | 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 | 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 |
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| S | Y | V | L | T | Q | P | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | N | N | I | G | S | K | T | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | V | Y | D | D | S | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | T | A | T | L | T | I | S | R | V | E | A | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | S | S | D | H | Y | V | F | G | T | G | T | K | V | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | R |
| Antigen type | protein |
| Antigen name | spike protein s1 |
| Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
| Antigen sequence | RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCS |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GGSISSY |
| CDRH2 | YYSGS |
| CDRH3 | SQRPDGNLYYFDY |
| CDRL1 | GGNNIGSKTVH |
| CDRL2 | DDSDRPS |
| CDRL3 | QVWDSSSDHYV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -58.99° |
| HC1 | 73.78° |
| HC2 | 121.23° |
| LC1 | 119.31° |
| LC2 | 81.42° |
| dc | 16.14Å |
| Fv Details | |
|---|---|
| Heavy chain | A |
| Light chain | B |
| 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| Q | V | Q | L | Q | E | S | G | P | G | L | V | K | P | S | E | T | L | S | L | T | C | T | V | S | G | G | S | I | S | S | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | Y | V | Y | Y | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | V | D | T | S | K | N | E | F | S | L | K | L | S | S | V | T | A | A | D | T | A | V | Y | Y | C | A | S | S | Q | R | P | D | G | N | L | Y | Y | F | D | Y | W | G | Q | G | T | 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 | 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 |
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| S | Y | V | L | T | Q | P | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | N | N | I | G | S | K | T | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | V | Y | D | D | S | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | T | A | T | L | T | I | S | R | V | E | A | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | S | S | D | H | Y | V | F | G | T | G | T | K | V | T | V | L |
| Antigen Details | |
|---|---|
| Antigen chains | C |
| Antigen type | protein |
| Antigen name | spike protein s1 |
| Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
| Antigen sequence | RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCS |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GGSISSY |
| CDRH2 | YYSGS |
| CDRH3 | SQRPDGNLYYFDY |
| CDRL1 | GGNNIGSKTVH |
| CDRL2 | DDSDRPS |
| CDRL3 | QVWDSSSDHYV |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -58.0° |
| HC1 | 73.98° |
| HC2 | 121.03° |
| LC1 | 117.75° |
| LC2 | 83.28° |
| dc | 16.0Å |
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]
