Lassa Gpc Trimer in complex with Fab 8.11G and Nanobody D5
| PDB | 8t5c |
| Species | HOMO SAPIENS; CAMELUS BACTRIANUS |
| Method | ELECTRON MICROSCOPY |
| Resolution | 4.7Å |
| Number of Fvs | 3 |
| In complex | True |
| Light chain type | unknown,Kappa |
| Has constant region | False |
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Display options: |
This PDB has 3 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV4 |
| Light subgroup | IGKV3 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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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 | 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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| E | I | V | L | T | Q | S | P | A | T | L | S | V | S | P | G | G | R | A | S | L | S | C | R | A | S | Q | S | I | G | D | K | L | S | W | Y | Q | Q | K | P | G | Q | A | P | R | L | V | I | Y | G | A | Y | T | R | A | T | D | I | S | P | R | F | S | G | S | R | S | G | T | D | F | N | L | T | I | S | R | M | Q | S | G | D | F | A | V | Y | F | C | Q | Q | Y | E | N | W | P | R | T | F | G | Q | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | a |
| Antigen type | protein |
| Antigen name | unknown |
| Antigen species | LASSA VIRUS JOSIAH |
| Antigen sequence | GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRCKAPAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEGGGYIPEAPRDGQAYVRKDGEWVLLSTFLGGLVPR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GVSTRNY |
| CDRH2 | FNIGT |
| CDRH3 | GFEYGDYTFDY |
| CDRL1 | RASQSIGDKLS |
| CDRL2 | GAYTRAT |
| CDRL3 | QQYENWPRT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -62.32° |
| HC1 | 75.88° |
| HC2 | 119.52° |
| LC1 | 120.67° |
| LC2 | 83.25° |
| dc | 16.47Å |
| Fv Details | |
|---|---|
| Heavy chain | E |
| Light chain | I |
| Heavy subgroup | IGHV4 |
| Light subgroup | IGKV3 |
| Species | HOMO SAPIENS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| 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 | 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 | S | I | S | G | V | S | T | R | N | Y | Y | W | S | W | I | R | Q | S | P | G | K | G | L | E | W | I | G | Y | I | F | N | I | G | T | T | N | Y | N | P | S | L | K | S | R | L | T | I | S | V | D | T | S | K | N | Q | F | S | L | K | I | T | S | V | T | A | A | D | T | A | V | Y | Y | C | A | S | G | F | E | Y | G | D | Y | T | F | D | Y | W | G | Q | G | T | P | 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 | 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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| E | I | V | L | T | Q | S | P | A | T | L | S | V | S | P | G | G | R | A | S | L | S | C | R | A | S | Q | S | I | G | D | K | L | S | W | Y | Q | Q | K | P | G | Q | A | P | R | L | V | I | Y | G | A | Y | T | R | A | T | D | I | S | P | R | F | S | G | S | R | S | G | T | D | F | N | L | T | I | S | R | M | Q | S | G | D | F | A | V | Y | F | C | Q | Q | Y | E | N | W | P | R | T | F | G | Q | G | T | K | L | E | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | b |
| Antigen type | protein |
| Antigen name | unknown |
| Antigen species | LASSA VIRUS JOSIAH |
| Antigen sequence | GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRCKAPAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEGGGYIPEAPRDGQAYVRKDGEWVLLSTFLGGLVPR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GVSTRNY |
| CDRH2 | FNIGT |
| CDRH3 | GFEYGDYTFDY |
| CDRL1 | RASQSIGDKLS |
| CDRL2 | GAYTRAT |
| CDRL3 | QQYENWPRT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -63.69° |
| HC1 | 76.08° |
| HC2 | 118.95° |
| LC1 | 119.47° |
| LC2 | 82.77° |
| dc | 16.25Å |
| Fv Details | |
|---|---|
| Heavy chain | D |
| Light chain | |
| Heavy subgroup | unknown |
| Light subgroup | unknown |
| Species | CAMELUS BACTRIANUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| A | W | Q | L | V | E | S | G | G | G | S | V | Q | P | G | G | S | L | T | L | T | C | Q | A | S | K | S | T | F | S | T | S | G | M | R | W | E | R | Q | A | Q | G | K | G | V | E | F | V | A | D | I | S | S | D | S | T | R | K | W | Y | S | D | S | V | K | G | R | F | T | I | S | R | S | N | W | W | R | T | V | T | L | Q | M | N | D | L | K | P | E | D | T | A | R | Y | Y | C | K | D | L | E | S | H | H | L | R | G | Q | G | T | Q | V | T | V | S | S |
| Antigen Details | |
|---|---|
| Antigen chains | A,C,B |
| Antigen type | protein |
| Antigen name | glycoprotein g2 |
| Antigen species | LASSA VIRUS JOSIAH |
| Antigen sequence | TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRRR/TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRRR/TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRRR |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | KSTFSTS |
| CDRH2 | SSDSTR |
| CDRH3 | LESHHL |
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]
