Crystal Structure of Sars-Cov-2 Spike Rbd in complex with Iy-2a Fab
PDB | 7ycn |
Species | HOMO SAPIENS |
Method | X-RAY DIFFRACTION |
Resolution | 2.85Å |
Number of Fvs | 4 |
In complex | True |
Light chain type | Lambda |
Has constant region | True |
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Display options: |
This PDB has 4 Fv(s).
Fv Details | |
---|---|
Heavy chain | K |
Light chain | L |
Heavy subgroup | IGHV4 |
Light subgroup | IGLV6 |
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 | 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 | V | E | W | G | A | G | L | L | K | P | S | E | T | L | S | L | T | C | A | V | Y | G | G | S | F | S | G | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | L | I | N | H | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | L | D | T | S | K | N | Q | F | S | L | K | L | T | S | V | T | A | A | D | T | A | V | Y | Y | C | A | R | G | L | G | I | F | G | V | V | T | L | S | D | V | W | G | Q | G | T | T | 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 | 30A | 30B | 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 | 68A | 68B | 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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N | F | M | L | T | Q | P | H | S | V | S | E | S | P | G | K | T | V | T | I | S | C | T | G | S | S | G | S | I | A | S | N | Y | V | Q | W | Y | Q | Q | R | P | G | S | A | P | T | T | V | I | Y | E | D | N | Q | R | P | S | G | V | P | D | R | F | S | G | S | I | D | S | S | S | N | S | A | S | L | T | I | S | G | L | R | T | E | D | E | A | D | Y | Y | C | Q | S | Y | D | S | G | I | W | V | F | G | G | G | T | K | L | T | V | L |
Antigen Details | |
---|---|
Antigen chains | J |
Antigen type | protein |
Antigen name | spike protein s1 |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GGSFSGY |
CDRH2 | NHSGS |
CDRH3 | GLGIFGVVTLSDV |
CDRL1 | TGSSGSIASNYVQ |
CDRL2 | EDNQRPS |
CDRL3 | QSYDSGIWV |
Orientation Angles (from ABangle) | |
---|---|
HL | -61.79° |
HC1 | 74.05° |
HC2 | 121.74° |
LC1 | 119.99° |
LC2 | 84.64° |
dc | 16.04Å |
Fv Details | |
---|---|
Heavy chain | E |
Light chain | F |
Heavy subgroup | IGHV4 |
Light subgroup | IGLV6 |
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 | V | E | W | G | A | G | L | L | K | P | S | E | T | L | S | L | T | C | A | V | Y | G | G | S | F | S | G | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | L | I | N | H | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | L | D | T | S | K | N | Q | F | S | L | K | L | T | S | V | T | A | A | D | T | A | V | Y | Y | C | A | R | G | L | G | I | F | G | V | V | T | L | S | D | V | W | G | Q | G | T | T | 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 | 30A | 30B | 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 | 68A | 68B | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N | F | M | L | T | Q | P | H | S | V | S | E | S | P | G | K | T | V | T | I | S | C | T | G | S | S | G | S | I | A | S | N | Y | V | Q | W | Y | Q | Q | R | P | G | S | A | P | T | T | V | I | Y | E | D | N | Q | R | P | S | G | V | P | D | R | F | S | G | S | I | D | S | S | S | N | S | A | S | L | T | I | S | G | L | R | T | E | D | E | A | D | Y | Y | C | Q | S | Y | D | S | G | I | W | V | F | G | G | G | T | K | L | T | V | L |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | spike protein s1 |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GGSFSGY |
CDRH2 | NHSGS |
CDRH3 | GLGIFGVVTLSDV |
CDRL1 | TGSSGSIASNYVQ |
CDRL2 | EDNQRPS |
CDRL3 | QSYDSGIWV |
Orientation Angles (from ABangle) | |
---|---|
HL | -64.37° |
HC1 | 74.02° |
HC2 | 118.33° |
LC1 | 119.04° |
LC2 | 84.1° |
dc | 15.78Å |
Fv Details | |
---|---|
Heavy chain | C |
Light chain | D |
Heavy subgroup | IGHV4 |
Light subgroup | IGLV6 |
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 | V | E | W | G | A | G | L | L | K | P | S | E | T | L | S | L | T | C | A | V | Y | G | G | S | F | S | G | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | L | I | N | H | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | L | D | T | S | K | N | Q | F | S | L | K | L | T | S | V | T | A | A | D | T | A | V | Y | Y | C | A | R | G | L | G | I | F | G | V | V | T | L | S | D | V | W | G | Q | G | T | T | 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 | 30A | 30B | 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 | 68A | 68B | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N | F | M | L | T | Q | P | H | S | V | S | E | S | P | G | K | T | V | T | I | S | C | T | G | S | S | G | S | I | A | S | N | Y | V | Q | W | Y | Q | Q | R | P | G | S | A | P | T | T | V | I | Y | E | D | N | Q | R | P | S | G | V | P | D | R | F | S | G | S | I | D | S | S | S | N | S | A | S | L | T | I | S | G | L | R | T | E | D | E | A | D | Y | Y | C | Q | S | Y | D | S | G | I | W | V | F | G | G | G | T | K | L | T | V | L |
Antigen Details | |
---|---|
Antigen chains | B |
Antigen type | protein |
Antigen name | spike protein s1 |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GGSFSGY |
CDRH2 | NHSGS |
CDRH3 | GLGIFGVVTLSDV |
CDRL1 | TGSSGSIASNYVQ |
CDRL2 | EDNQRPS |
CDRL3 | QSYDSGIWV |
Orientation Angles (from ABangle) | |
---|---|
HL | -62.08° |
HC1 | 73.97° |
HC2 | 120.73° |
LC1 | 118.81° |
LC2 | 84.12° |
dc | 15.97Å |
Fv Details | |
---|---|
Heavy chain | H |
Light chain | I |
Heavy subgroup | IGHV4 |
Light subgroup | IGLV6 |
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 | V | E | W | G | A | G | L | L | K | P | S | E | T | L | S | L | T | C | A | V | Y | G | G | S | F | S | G | Y | Y | W | S | W | I | R | Q | P | P | G | K | G | L | E | W | I | G | L | I | N | H | S | G | S | T | N | Y | N | P | S | L | K | S | R | V | T | I | S | L | D | T | S | K | N | Q | F | S | L | K | L | T | S | V | T | A | A | D | T | A | V | Y | Y | C | A | R | G | L | G | I | F | G | V | V | T | L | S | D | V | W | G | Q | G | T | T | 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 | 30A | 30B | 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 | 68A | 68B | 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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N | F | M | L | T | Q | P | H | S | V | S | E | S | P | G | K | T | V | T | I | S | C | T | G | S | S | G | S | I | A | S | N | Y | V | Q | W | Y | Q | Q | R | P | G | S | A | P | T | T | V | I | Y | E | D | N | Q | R | P | S | G | V | P | D | R | F | S | G | S | I | D | S | S | S | N | S | A | S | L | T | I | S | G | L | R | T | E | D | E | A | D | Y | Y | C | Q | S | Y | D | S | G | I | W | V | F | G | G | G | T | K | L | T | V | L |
Antigen Details | |
---|---|
Antigen chains | G |
Antigen type | protein |
Antigen name | spike protein s1 |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GGSFSGY |
CDRH2 | NHSGS |
CDRH3 | GLGIFGVVTLSDV |
CDRL1 | TGSSGSIASNYVQ |
CDRL2 | EDNQRPS |
CDRL3 | QSYDSGIWV |
Orientation Angles (from ABangle) | |
---|---|
HL | -63.08° |
HC1 | 74.34° |
HC2 | 119.89° |
LC1 | 118.33° |
LC2 | 83.92° |
dc | 15.9Å |
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]