7BEP
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, F (E, C) | Spike glycoprotein | polymer | 205 | 23150.9 | 2 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) | S glycoprotein,E2,Peplomer protein |
| 2 | B, G (A, D) | COVOX-384 heavy chain | polymer | 243 | 26089.5 | 2 | Homo sapiens | ||
| 3 | C, H (B, F) | COVOX-384 light chain | polymer | 227 | 24526.4 | 2 | Homo sapiens | ||
| 4 | D, I (H, G) | S309 heavy chain | polymer | 232 | 24817.7 | 2 | Homo sapiens | ||
| 5 | E, J (L, I) | S309 light chain | polymer | 214 | 23204.7 | 2 | Homo sapiens | ||
| 6 | K, L (J, K) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | 1057.0 | 2 | In PDB GlyTouCan (G82348BZ) | |||
| 7 | BA, M, NA, V, X (C, E, G, H) | IMIDAZOLE | non-polymer | 69.1 | 5 | Chemie (IMD) | |||
| 8 | CA, DA, EA, HA, N... (C, D, F, A, I...) | CHLORIDE ION | non-polymer | 35.5 | 10 | Chemie (CL) | |||
| 9 | GA, P (D, A) | GLUTAMIC ACID | non-polymer | 147.1 | 2 | Chemie (GLU) | |||
| 10 | AA, JA, MA, OA, Q... (L, F, G, A, H) | GLYCINE | non-polymer | 75.1 | 6 | Chemie (GLY) | |||
| 11 | R (B) | TRIETHYLENE GLYCOL | non-polymer | 150.2 | 1 | Chemie (PGE) | |||
| 12 | IA, KA, LA, U (F, G, H) | GLYCEROL | non-polymer | 92.1 | 4 | Chemie (GOL) | |||
| 13 | PA, Z (I, L) | TETRAETHYLENE GLYCOL | non-polymer | 194.2 | 2 | Chemie (PG4) | |||
| 14 | FA (D) | DI(HYDROXYETHYL)ETHER | non-polymer | 106.1 | 1 | Chemie (PEG) | |||
| 15 | RA, SA, TA, UA, VA... (E, A, H, L, C...) | water | water | 18.0 | 18 | Chemie (HOH) |
Sequence modifications
E, C: 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 | 10 |
| Total formula weight | 243578.4 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 2113.9 | |
| Non-Polymers* | Number of molecules | 31 |
| Total formula weight | 2457.7 | |
| All* | Total formula weight | 248150.0 |
