7BEM
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (H) | COVOX-269 Vh domain | polymer | 135 | 13950.3 | 1 | Homo sapiens | ||
| 2 | B (L) | COVOX-269 Vl domain | polymer | 149 | 15553.2 | 1 | Homo sapiens | ||
| 3 | C (E) | Spike glycoprotein | polymer | 205 | 23150.9 | 1 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) | S glycoprotein,E2,Peplomer protein |
| 4 | D (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 1 | In PDB GlyTouCan (G21290RB) | |||
| 5 | E, I (H, E) | GLYCEROL | non-polymer | 92.1 | 2 | Chemie (GOL) | |||
| 6 | F, N (H, E) | CHLORIDE ION | non-polymer | 35.5 | 2 | Chemie (CL) | |||
| 7 | G, H (L) | PHOSPHATE ION | non-polymer | 95.0 | 2 | Chemie (PO4) | |||
| 8 | J, K, L, M (E) | PROLINE | non-polymer | 115.1 | 4 | Chemie (PRO) | |||
| 9 | O, P, Q (H, L, E) | water | water | 18.0 | 33 | Chemie (HOH) |
Sequence modifications
E: 333 - 528 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Glu 324 | - | expression tag |
| Thr 325 | - | expression tag |
| Gly 326 | - | expression tag |
| His 327 | - | expression tag |
| His 328 | - | expression tag |
| His 329 | - | expression tag |
| His 330 | - | expression tag |
| His 331 | - | expression tag |
| His 332 | - | expression tag |
| Lys 527 | Pro 527 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 52654.5 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 570.5 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 905.6 | |
| All* | Total formula weight | 54130.5 |
