7AKD
Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment
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 | 1286 | 141680.6 | 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 (D, H) | 47D11 neutralizing antibody heavy chain | polymer | 121 | 13205.8 | 2 | Homo sapiens | ||
| 3 | E, G (E, L) | 47D11 neutralizing antibody light chain | polymer | 106 | 11350.6 | 2 | Homo sapiens | ||
| 4 | H, K, L, M, P... (F, J, K, M, P...) | 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 | I, J, N (G, I, N) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 3 | In PDB GlyTouCan (G15407YE) | |||
| 6 | O (O) | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(3-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 910.8 | 1 | ||||
| 7 | S (S) | 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) | |||
| 8 | T (T) | 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 (G29616NS) | |||
| 9 | U (U) | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose | branched | 342.3 | 1 | In PDB GlyTouCan (G77384RA) | |||
| 10 | AA, AB, BA, BB, CA... (A, C, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 28 | Chemie (NAG) | |||
| 11 | CB, HA, NA (C, A, B) | alpha-L-fucopyranose | non-polymer | 164.2 | 3 | Chemie (FUC) | |||
| 12 | DB, EB (D, H) | alpha-D-mannopyranose | non-polymer | 180.2 | 2 | Chemie (MAN) |
Sequence modifications
A, B, C: 1 - 1208 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Gly 682 | Arg 682 | conflict |
| Ser 683 | Arg 683 | conflict |
| Ser 685 | Arg 685 | conflict |
| Pro 986 | Lys 986 | conflict |
| Pro 987 | Val 987 | conflict |
| Gly 1209 | - | expression tag |
| Ser 1210 | - | expression tag |
| Gly 1211 | - | expression tag |
| Tyr 1212 | - | expression tag |
| Ile 1213 | - | expression tag |
| Pro 1214 | - | expression tag |
| Glu 1215 | - | expression tag |
| Ala 1216 | - | expression tag |
| Pro 1217 | - | expression tag |
| Arg 1218 | - | expression tag |
| Asp 1219 | - | expression tag |
| Gly 1220 | - | expression tag |
| Gln 1221 | - | expression tag |
| Ala 1222 | - | expression tag |
| Tyr 1223 | - | expression tag |
| Val 1224 | - | expression tag |
| Arg 1225 | - | expression tag |
| Lys 1226 | - | expression tag |
| Asp 1227 | - | expression tag |
| Gly 1228 | - | expression tag |
| Glu 1229 | - | expression tag |
| Trp 1230 | - | expression tag |
| Val 1231 | - | expression tag |
| Leu 1232 | - | expression tag |
| Leu 1233 | - | expression tag |
| Ser 1234 | - | expression tag |
| Thr 1235 | - | expression tag |
| Phe 1236 | - | expression tag |
| Leu 1237 | - | expression tag |
| Gly 1238 | - | expression tag |
| Arg 1239 | - | expression tag |
| Ser 1240 | - | expression tag |
| Leu 1241 | - | expression tag |
| Glu 1242 | - | expression tag |
| Val 1243 | - | expression tag |
| Leu 1244 | - | expression tag |
| Phe 1245 | - | expression tag |
| Gln 1246 | - | expression tag |
| Gly 1247 | - | expression tag |
| Pro 1248 | - | expression tag |
| Gly 1249 | - | expression tag |
| Gly 1250 | - | expression tag |
| Ser 1251 | - | expression tag |
| Ala 1252 | - | expression tag |
| Gly 1253 | - | expression tag |
| Gly 1254 | - | expression tag |
| Ser 1255 | - | expression tag |
| Ala 1256 | - | expression tag |
| Gly 1257 | - | expression tag |
| Trp 1258 | - | expression tag |
| Ser 1259 | - | expression tag |
| His 1260 | - | expression tag |
| Pro 1261 | - | expression tag |
| Gln 1262 | - | expression tag |
| Phe 1263 | - | expression tag |
| Glu 1264 | - | expression tag |
| Lys 1265 | - | expression tag |
| Gly 1266 | - | expression tag |
| Gly 1267 | - | expression tag |
| Gly 1268 | - | expression tag |
| Ser 1269 | - | expression tag |
| Gly 1270 | - | expression tag |
| Gly 1271 | - | expression tag |
| Gly 1272 | - | expression tag |
| Gly 1273 | - | expression tag |
| Ser 1274 | - | expression tag |
| Gly 1275 | - | expression tag |
| Gly 1276 | - | expression tag |
| Ser 1277 | - | expression tag |
| Ala 1278 | - | expression tag |
| Trp 1279 | - | expression tag |
| Ser 1280 | - | expression tag |
| His 1281 | - | expression tag |
| Pro 1282 | - | expression tag |
| Gln 1283 | - | expression tag |
| Phe 1284 | - | expression tag |
| Glu 1285 | - | expression tag |
| Lys 1286 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 474154.6 | |
| Branched | Number of molecules | 17 |
| Total formula weight | 9046.4 | |
| Non-Polymers* | Number of molecules | 33 |
| Total formula weight | 7046.6 | |
| All* | Total formula weight | 490247.6 |
