6WPT
Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, C (A, B, C) | spike glycoprotein | polymer | 1281 | 141532.8 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) | S glycoprotein,E2,Peplomer protein |
| 2 | D, F (H, D) | S309 neutralizing antibody heavy chain | polymer | 127 | 14005.5 | 2 | Homo sapiens (Human) | ||
| 3 | E, G (L, E) | S309 neutralizing antibody light chain | polymer | 107 | 11444.7 | 2 | Homo sapiens (Human) | ||
| 4 | H, I, J, L, M... (F, G, I, K, M...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 10 | In PDB GlyTouCan (G42666HT) | |||
| 5 | K (J) | 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 | S (S) | 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 | AA, AB, BA, BB, CA... (A, C, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 35 | Chemie (NAG) |
Sequence modifications
A, B, C: -18 - 13 (PDB: 6WPT)
A, B, C: 14 - 1211 (UniProt: P0DTC2)
A, B, C: 14 - 1211 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Ser 682 | Arg 682 | engineered mutation |
| Gly 683 | Arg 683 | engineered mutation |
| Gly 685 | Arg 685 | engineered mutation |
| Pro 986 | Lys 986 | engineered mutation |
| Pro 987 | Val 987 | engineered mutation |
| Gly 1212 | - | expression tag |
| Ser 1213 | - | expression tag |
| Gly 1214 | - | expression tag |
| Arg 1215 | - | expression tag |
| Glu 1216 | - | expression tag |
| Asn 1217 | - | expression tag |
| Leu 1218 | - | expression tag |
| Tyr 1219 | - | expression tag |
| Phe 1220 | - | expression tag |
| Gln 1221 | - | expression tag |
| Gly 1222 | - | expression tag |
| Gly 1223 | - | expression tag |
| Gly 1224 | - | expression tag |
| Gly 1225 | - | expression tag |
| Ser 1226 | - | expression tag |
| Gly 1227 | - | expression tag |
| Tyr 1228 | - | expression tag |
| Ile 1229 | - | expression tag |
| Pro 1230 | - | expression tag |
| Glu 1231 | - | expression tag |
| Ala 1232 | - | expression tag |
| Pro 1233 | - | expression tag |
| Arg 1234 | - | expression tag |
| Asp 1235 | - | expression tag |
| Gly 1236 | - | expression tag |
| Gln 1237 | - | expression tag |
| Ala 1238 | - | expression tag |
| Tyr 1239 | - | expression tag |
| Val 1240 | - | expression tag |
| Arg 1241 | - | expression tag |
| Lys 1242 | - | expression tag |
| Asp 1243 | - | expression tag |
| Gly 1244 | - | expression tag |
| Glu 1245 | - | expression tag |
| Trp 1246 | - | expression tag |
| Val 1247 | - | expression tag |
| Leu 1248 | - | expression tag |
| Leu 1249 | - | expression tag |
| Ser 1250 | - | expression tag |
| Thr 1251 | - | expression tag |
| Phe 1252 | - | expression tag |
| Leu 1253 | - | expression tag |
| Gly 1254 | - | expression tag |
| His 1255 | - | expression tag |
| His 1256 | - | expression tag |
| His 1257 | - | expression tag |
| His 1258 | - | expression tag |
| His 1259 | - | expression tag |
| His 1260 | - | expression tag |
| His 1261 | - | expression tag |
| His 1262 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 475498.8 | |
| Branched | Number of molecules | 12 |
| Total formula weight | 6033.7 | |
| Non-Polymers* | Number of molecules | 35 |
| Total formula weight | 7742.3 | |
| All* | Total formula weight | 489274.7 |
