7LY3
Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab
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) | Spike protein S1 | polymer | 335 | 37705.7 | 2 | UniProt (P0DTC2) Pfam (PF16451) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | |
| 2 | C, F (D, F) | S2M28 Fab Heavy Chain | polymer | 221 | 23778.6 | 2 | Homo sapiens (Human) | ||
| 3 | D, E (C, E) | S2M28 Fab Light Chain | polymer | 212 | 22620.0 | 2 | Homo sapiens (Human) | ||
| 4 | G, I, M (G, I, M) | 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 | 3 | In PDB GlyTouCan (G32152BH) | |||
| 5 | H, J, N, O (H, J, N, O) | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 367.3 | 4 | In PDB GlyTouCan (G86851RC) | |||
| 6 | K, L (K, L) | 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 | 2 | In PDB GlyTouCan (G00395TQ) | |||
| 7 | P, Q, T, U, V (A, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 5 | Chemie (NAG) | |||
| 8 | R, W (A, B) | UNKNOWN ATOM OR ION | non-polymer | 35.5 | 2 | Chemie (UNX) | |||
| 9 | S, X (A, B) | Xylitol | non-polymer | 152.1 | 2 | Chemie (XYL) | |||
| 10 | Y, Z (D, F) | SULFATE ION | non-polymer | 96.1 | 2 | Chemie (SO4) |
Sequence modifications
A, B: 14 - 307 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Met -18 | - | initiating methionine |
| Gly -17 | - | expression tag |
| Ile -16 | - | expression tag |
| Leu -15 | - | expression tag |
| Pro -14 | - | expression tag |
| Ser -13 | - | expression tag |
| Pro -12 | - | expression tag |
| Gly -11 | - | expression tag |
| Met -10 | - | expression tag |
| Pro -9 | - | expression tag |
| Ala -8 | - | expression tag |
| Leu -7 | - | expression tag |
| Leu -6 | - | expression tag |
| Ser -5 | - | expression tag |
| Leu -4 | - | expression tag |
| Val -3 | - | expression tag |
| Ser -2 | - | expression tag |
| Leu -1 | - | expression tag |
| Leu 0 | - | expression tag |
| Ser 1 | - | expression tag |
| Val 2 | - | expression tag |
| Leu 3 | - | expression tag |
| Leu 4 | - | expression tag |
| Met 5 | - | expression tag |
| Gly 6 | - | expression tag |
| Cys 7 | - | expression tag |
| Val 8 | - | expression tag |
| Ala 9 | - | expression tag |
| Glu 10 | - | expression tag |
| Thr 11 | - | expression tag |
| Gly 12 | - | expression tag |
| Thr 13 | - | expression tag |
| Ala 303 | Leu 303 | conflict |
| Ala 308 | - | expression tag |
| His 309 | - | expression tag |
| His 310 | - | expression tag |
| His 311 | - | expression tag |
| His 312 | - | expression tag |
| His 313 | - | expression tag |
| His 314 | - | expression tag |
| His 315 | - | expression tag |
| His 316 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 6 |
| Total formula weight | 168208.6 | |
| Branched | Number of molecules | 9 |
| Total formula weight | 5457.1 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 1673.4 | |
| All* | Total formula weight | 175339.0 |
