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 | spike glycoprotein | polymer | 1281 | 141532.8 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) | S glycoprotein,E2,Peplomer protein |
2 | H, D | S309 neutralizing antibody heavy chain | polymer | 127 | 14005.5 | 2 | Homo sapiens (Human) | ||
3 | L, E | S309 neutralizing antibody light chain | polymer | 107 | 11444.7 | 2 | Homo sapiens (Human) | ||
4 | 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 | 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 | 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 | 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 |