Crystal Structure of Sars-Cov-2 Receptor Binding Domain in complex with Sars-Cov-2 Reactive Human antibody Cr3022
PDB | 8fah |
Species | HOMO SAPIENS |
Method | X-RAY DIFFRACTION |
Resolution | 4.22Å |
Number of Fvs | 1 |
In complex | True |
Light chain type | Kappa |
Has constant region | True |
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Display options: |
This PDB has 1 Fv(s).
Fv Details | |
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Heavy chain | H |
Light chain | L |
Heavy subgroup | IGHV5 |
Light subgroup | IGKV4 |
Species | HOMO SAPIENS |
In complex? | True |
scFv? | False |
Has constant domain? | True |
Numbered Sequences (chothia) |
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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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | V | Q | S | G | T | E | V | K | K | P | G | E | S | L | K | I | S | C | K | G | S | G | Y | G | F | I | T | Y | W | I | G | W | V | R | Q | M | P | G | K | G | L | E | W | M | G | I | I | Y | P | G | D | S | E | T | R | Y | S | P | S | F | Q | G | Q | V | T | I | S | A | D | K | S | I | N | T | A | Y | L | Q | W | S | S | L | K | A | S | D | T | A | I | Y | Y | C | A | G | G | S | G | I | S | T | P | M | D | V | W | G | Q | G | T | T | V | T | 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 | 29 | 30 | 30A | 30B | 30C | 30D | 30E | 30F | 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 |
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D | I | V | M | T | Q | S | P | D | S | L | A | V | S | L | G | E | R | A | T | I | N | C | K | S | S | Q | S | V | L | Y | S | S | I | N | K | N | Y | L | A | W | Y | Q | Q | K | P | G | Q | P | P | K | L | L | I | Y | W | A | S | T | R | E | S | G | V | P | D | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | S | S | L | Q | A | E | D | V | A | V | Y | Y | C | Q | Q | Y | Y | S | T | P | Y | T | F | G | Q | G | T | K | V | E | I | K |
Antigen Details | |
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Antigen chains | A |
Antigen type | protein |
Antigen name | spike protein s1 |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHHHHH |
CDR Sequences (chothia definition) | |
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CDRH1 | GYGFITY |
CDRH2 | YPGDSE |
CDRH3 | GSGISTPMDV |
CDRL1 | KSSQSVLYSSINKNYLA |
CDRL2 | WASTRES |
CDRL3 | QQYYSTPYT |
Orientation Angles (from ABangle) | |
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HL | -55.29° |
HC1 | 70.57° |
HC2 | 115.68° |
LC1 | 124.12° |
LC2 | 82.85° |
dc | 16.59Å |
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]