9XA0
Structure of the Omicron KP.3.1.1 variant Spike N-terminal domain(NTD)in complex with the C1717 Fab and S2L20 Fab
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (C) | Spike glycoprotein | polymer | 297 | 33807.0 | 1 | UniProt (P0DTC2) Pfam (PF16451) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | B (D) | C1717 heavy chain | polymer | 233 | 24979.0 | 1 | Homo sapiens | ||
| 3 | C (E) | C1717 light chain | polymer | 217 | 22792.1 | 1 | Homo sapiens | ||
| 4 | D (A) | S2L20 heavy chain | polymer | 235 | 25449.4 | 1 | Homo sapiens | ||
| 5 | E (B) | S2L20 light chain | polymer | 215 | 23676.2 | 1 | Homo sapiens | ||
| 6 | F, H (F, H) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
| 7 | G (G) | 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) | |||
| 8 | I (I) | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 367.3 | 1 | In PDB GlyTouCan (G86851RC) | |||
| 9 | J, K (J, K) | 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) | |||
| 10 | L (C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 1 | Chemie (NAG) PubChem (24139) |
Sequence modifications
C: 11 - 301 (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 |
| - | Ser 31 | deletion |
| Leu 50 | Ser 50 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Phe 125 | Val 127 | conflict |
| Asp 140 | Gly 142 | variant |
| - | Tyr 145 | deletion |
| Ser 154 | Phe 157 | conflict |
| Gly 155 | Arg 158 | conflict |
| - | Asn 211 | deletion |
| Ile 208 | Leu 212 | variant |
| Gly 209 | Val 213 | variant |
| Phe 212 | Leu 216 | conflict |
| Asn 241 | His 245 | conflict |
| Asp 260 | Ala 264 | conflict |
| His 302 | - | expression tag |
| His 303 | - | expression tag |
| His 304 | - | expression tag |
| His 305 | - | expression tag |
| His 306 | - | expression tag |
| His 307 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 130703.8 | |
| Branched | Number of molecules | 6 |
| Total formula weight | 3252.1 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 221.2 | |
| All* | Total formula weight | 134177.0 |
