7ORB
Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 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 (R, X) | Spike protein S1 | polymer | 205 | 23194.9 | 2 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | |
| 2 | B, G (H, C) | COVOX-253 Fab heavy chain | polymer | 228 | 24371.4 | 2 | Homo sapiens | ||
| 3 | C, H (L, D) | COVOX-253 Fab light chain | polymer | 215 | 23256.6 | 2 | Homo sapiens | ||
| 4 | D, I (A, E) | COVOX-75 Fab heavy chain | polymer | 232 | 24821.8 | 2 | Homo sapiens | ||
| 5 | E, J (B, F) | COVOX-75 Fab light chain | polymer | 214 | 23244.9 | 2 | Homo sapiens | ||
| 6 | K (G) | 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 | 1 | In PDB GlyTouCan (G82348BZ) | |||
| 7 | L (I) | 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) | |||
| 8 | M (J) | 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 | 894.8 | 1 | In PDB GlyTouCan (G00395TQ) | |||
| 9 | N (K) | 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 | 1 | In PDB GlyTouCan (G32152BH) | |||
| 10 | AA, BA, CA, FA, IA... (B, X, C, D, E...) | GLYCEROL | non-polymer | 92.1 | 16 | Chemie (GOL) | |||
| 11 | DA, EA, KA, P (X, E, R) | DI(HYDROXYETHYL)ETHER | non-polymer | 106.1 | 4 | Chemie (PEG) | |||
| 12 | GA, PA, QA, T (C, E, H) | CHLORIDE ION | non-polymer | 35.5 | 4 | Chemie (CL) | |||
| 13 | HA, U (D, L) | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL | non-polymer | 122.1 | 2 | Chemie (TRS) | |||
| 14 | NA, OA, Y (E, A) | PHOSPHATE ION | non-polymer | 95.0 | 3 | Chemie (PO4) | |||
| 15 | MA (E) | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL | non-polymer | 209.2 | 1 | Chemie (BTB) | |||
| 16 | AB, BB, SA, TA, UA... (E, F, R, H, L...) | water | water | 18.0 | 417 | Chemie (HOH) |
Sequence modifications
R, X: 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 |
| Arg 452 | Leu 452 | engineered mutation |
| Lys 527 | Pro 527 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 10 |
| Total formula weight | 237779.3 | |
| Branched | Number of molecules | 4 |
| Total formula weight | 3255.0 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 2778.2 | |
| All* | Total formula weight | 243812.6 |
