7F5H
The crystal structure of RBD-Nanobody complex, DL28 (SC4)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B (A, B) | SARS-CoV-2 Spike Receptor-Binding Domain (RBD) | polymer | 213 | 23747.6 | 2 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) | S glycoprotein,E2,Peplomer protein |
| 2 | C, D (C, D) | Nanobody DL28 | polymer | 143 | 15525.8 | 2 | Vicugna pacos | ||
| 3 | E, F (E, F) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 732.7 | 2 | In PDB GlyTouCan (G32152BH) | |||
| 4 | G, H, J, K (A, B, C, D) | GLYCEROL | non-polymer | 92.1 | 4 | Chemie (GOL) | |||
| 5 | I (B) | PHOSPHATE ION | non-polymer | 95.0 | 1 | Chemie (PO4) | |||
| 6 | L, M, N, O (A, B, C, D) | water | water | 18.0 | 21 | Chemie (HOH) |
Sequence modifications
A, B: 330 - 531 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Ala 327 | - | expression tag |
| Gly 328 | - | expression tag |
| Ser 329 | - | expression tag |
| Gly 532 | - | expression tag |
| Thr 533 | - | expression tag |
| Leu 534 | - | expression tag |
| Glu 535 | - | expression tag |
| Val 536 | - | expression tag |
| Leu 537 | - | expression tag |
| Phe 538 | - | expression tag |
| Gln 539 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 4 |
| Total formula weight | 78546.9 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 1465.4 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 463.3 | |
| All* | Total formula weight | 80475.6 |
