Cryo-Em Structure of Ebv Ghgl-Gp42 in complex with Mabs 3E8 and 5E3 (Localized Refinement)
| PDB | 7yoy |
| Species | ORYCTOLAGUS CUNICULUS |
| Method | ELECTRON MICROSCOPY |
| Resolution | 3.64Å |
| Number of Fvs | 2 |
| In complex | True |
| Light chain type | Kappa |
| Has constant region | False |
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Display options: |
This PDB has 2 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | E |
| Light chain | I |
| Heavy subgroup | IGHV1 |
| Light subgroup | IGKV1 |
| Species | ORYCTOLAGUS CUNICULUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 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 | 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 | 100H | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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| V | E | E | S | G | G | R | L | V | T | P | G | T | P | L | T | L | T | C | T | V | S | G | F | S | L | S | T | Y | A | M | S | W | V | R | Q | A | P | G | K | G | L | E | W | I | G | T | I | S | A | S | D | T | T | Y | F | A | N | W | T | K | G | R | F | T | I | S | K | A | S | T | T | V | D | L | K | I | T | S | P | T | T | E | D | T | A | T | F | F | C | A | R | F | S | A | Y | E | S | N | R | D | Y | F | D | T | F | D | P | W | G | P | G | T | L | 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 | 95A | 95B | 95C | 95D | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| D | V | V | M | T | Q | T | P | S | P | V | S | A | A | V | G | G | T | V | T | I | K | C | Q | A | S | Q | N | I | Y | R | D | L | A | W | Y | Q | Q | N | P | G | Q | P | P | K | L | L | I | Y | G | A | S | N | L | A | S | G | V | P | S | R | F | S | G | S | G | S | G | T | E | Y | I | L | T | I | S | D | L | E | C | A | D | A | A | T | Y | Y | C | Q | C | S | A | Y | G | S | G | Y | A | A | H | A | F | G | G | G | T | K | V | D | I | K |
| Antigen Details | |
|---|---|
| Antigen chains | C |
| Antigen type | protein |
| Antigen name | soluble gp42 |
| Antigen species | HUMAN GAMMAHERPESVIRUS 4 |
| Antigen sequence | FQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNS |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSLSTY |
| CDRH2 | SASDT |
| CDRH3 | FSAYESNRDYFDTFDP |
| CDRL1 | QASQNIYRDLA |
| CDRL2 | GASNLAS |
| CDRL3 | QCSAYGSGYAAHA |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -57.95° |
| HC1 | 73.98° |
| HC2 | 117.81° |
| LC1 | 120.35° |
| LC2 | 81.72° |
| dc | 16.51Å |
| Fv Details | |
|---|---|
| Heavy chain | F |
| Light chain | J |
| Heavy subgroup | IGHV1 |
| Light subgroup | IGKV1 |
| Species | ORYCTOLAGUS CUNICULUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| Numbered Sequences (chothia) |
|---|
Heavy chain
| 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 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| V | K | E | S | G | G | R | L | V | T | P | G | T | P | L | T | L | T | C | T | A | S | G | F | S | L | S | S | Y | W | M | S | W | V | R | Q | A | R | G | K | G | L | E | W | I | G | T | A | T | A | G | G | S | A | W | Y | A | S | W | A | K | G | R | F | T | I | S | R | T | S | T | T | V | E | L | R | M | T | S | L | T | T | E | D | T | A | T | Y | F | C | A | R | D | P | P | G | H | S | G | L | W | G | R | G | T | L | 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 | 95A | 95B | 95C | 95D | 95E | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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| D | L | V | M | T | Q | T | P | A | S | V | E | A | A | V | G | G | T | V | T | I | K | C | Q | A | S | E | S | I | G | N | A | L | A | W | Y | Q | Q | K | P | G | Q | P | P | K | L | L | I | Y | D | T | S | N | L | A | S | G | V | S | S | R | F | R | G | S | G | S | G | T | Q | F | T | L | T | I | S | D | L | E | C | A | D | A | A | T | Y | Y | C | Q | T | Y | Y | Y | S | G | V | T | T | T | Y | Q | A | F | G | G | G | T | E | V | D | V | K |
| Antigen Details | |
|---|---|
| Antigen chains | C |
| Antigen type | protein |
| Antigen name | soluble gp42 |
| Antigen species | HUMAN GAMMAHERPESVIRUS 4 |
| Antigen sequence | FQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNS |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSLSSY |
| CDRH2 | TAGGS |
| CDRH3 | DPPGHSGL |
| CDRL1 | QASESIGNALA |
| CDRL2 | DTSNLAS |
| CDRL3 | QTYYYSGVTTTYQA |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -52.74° |
| HC1 | 72.73° |
| HC2 | 119.3° |
| LC1 | 118.73° |
| LC2 | 82.93° |
| dc | 16.43Å |
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]
