Sars-Cov-2 Spike Rbd in complex with Neutralizing Fab Sars2-38 (Local Refinement)
| PDB | 7mkm |
| Species | MUS MUSCULUS |
| Method | ELECTRON MICROSCOPY |
| Resolution | 3.16Å |
| Number of Fvs | 1 |
| In complex | True |
| Light chain type | Kappa |
| Has constant region | False |
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Display options: |
This PDB has 1 Fv(s).
| Fv Details | |
|---|---|
| Heavy chain | H |
| Light chain | L |
| Heavy subgroup | IGHV2 |
| Light subgroup | IGKV4 |
| Species | MUS MUSCULUS |
| In complex? | True |
| scFv? | False |
| Has constant domain? | False |
| Numbered Sequences (chothia) |
|---|
Heavy chain
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Light chain
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| Q | I | V | L | T | Q | S | P | A | I | M | S | A | S | P | G | E | K | V | T | M | T | C | S | A | S | S | T | V | S | F | I | Y | W | Y | Q | Q | K | P | G | S | S | P | R | L | L | I | Y | D | T | S | N | P | A | S | G | V | P | V | R | F | S | G | S | G | C | G | T | S | Y | Y | L | T | I | S | R | M | E | A | E | D | A | A | T | Y | Y | C | Q | Q | W | N | T | Y | P | L | T | F | G | A | G | T | K | L | E | L |
| Antigen Details | |
|---|---|
| Antigen chains | A |
| Antigen type | protein |
| Antigen name | spike protein s1 |
| Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
| Antigen sequence | TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHA |
| CDR Sequences (chothia definition) | |
|---|---|
| CDRH1 | GFSLTRY |
| CDRH2 | WADGS |
| CDRH3 | DGRGYDDY |
| CDRL1 | SASSTVSFIY |
| CDRL2 | DTSNPAS |
| CDRL3 | QQWNTYPLT |
| Orientation Angles (from ABangle) | |
|---|---|
| HL | -50.05° |
| HC1 | 75.41° |
| HC2 | 114.55° |
| LC1 | 120.13° |
| LC2 | 81.71° |
| dc | 18.1Å |
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]
