9X9Z
Structure of the Omicron BA.2.86 variant Spike N-terminal domain(NTD)in complex with the antibody Fab fragment, C1717
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Spike protein S1 | polymer | 295 | 33620.8 | 1 | UniProt (P0DTC2) Pfam (PF16451) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | |
| 2 | B (H) | C1717 heavy chain | polymer | 233 | 24979.0 | 1 | Homo sapiens | ||
| 3 | C (L) | C1717 light chain | polymer | 216 | 22677.0 | 1 | Homo sapiens | ||
| 4 | D, G (B, E) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 2 | In PDB GlyTouCan (G21290RB) | |||
| 5 | E (C) | 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) | |||
| 6 | F, H, I (D, F, G) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 3 | In PDB GlyTouCan (G42666HT) | |||
| 7 | J (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) PubChem (24139) | |||
| 8 | K, L, M (A, H, L) | water | water | 18.0 | 121 | Chemie (HOH) |
Sequence modifications
A: 14 - 302 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Met 17 | - | insertion |
| Pro 18 | - | insertion |
| Leu 19 | - | insertion |
| Phe 20 | - | insertion |
| Ile 23 | Thr 19 | variant |
| Thr 25 | Arg 21 | conflict |
| - | Leu 24 | deletion |
| - | Pro 25 | deletion |
| - | Pro 26 | deletion |
| Ser 28 | Ala 27 | variant |
| Leu 51 | Ser 50 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Phe 126 | Val 127 | conflict |
| Asp 141 | Gly 142 | variant |
| - | Tyr 145 | deletion |
| Ser 155 | Phe 157 | conflict |
| Gly 156 | Arg 158 | conflict |
| - | Asn 211 | deletion |
| Ile 209 | Leu 212 | variant |
| Gly 210 | Val 213 | variant |
| Phe 213 | Leu 216 | conflict |
| Asn 242 | His 245 | conflict |
| Asp 261 | Ala 264 | conflict |
| His 303 | - | expression tag |
| His 304 | - | expression tag |
| His 305 | - | expression tag |
| His 306 | - | expression tag |
| His 307 | - | expression tag |
| His 308 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 81276.8 | |
| Branched | Number of molecules | 6 |
| Total formula weight | 3147.0 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 221.2 | |
| All* | Total formula weight | 84645.0 |
