6XCM
Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
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 | 1259 | 139789.0 | 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, E (H, N) | C105 Fab Heavy Chain | polymer | 230 | 24662.5 | 2 | Homo sapiens (Human) | ||
| 3 | F, G (L, S) | C105 Fab Light Chain | polymer | 217 | 22893.2 | 2 | Homo sapiens (Human) | ||
| 4 | H, I, K, L, N... (D, E, G, I, K...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 9 | In PDB GlyTouCan (G42666HT) | |||
| 5 | J (F) | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 367.3 | 1 | In PDB GlyTouCan (G86851RC) | |||
| 6 | M, T (J, T) | 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) | |||
| 7 | R (Q) | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 1 | In PDB GlyTouCan (G15407YE) | |||
| 8 | AA, BA, CA, DA, EA... (A, B, C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 30 | Chemie (NAG) |
Sequence modifications
A, B, C: 1 - 1213 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Glu 607 | Gln 607 | conflict |
| Pro 986 | Lys 986 | conflict |
| Pro 987 | Val 987 | conflict |
| Ser 1214 | - | expression tag |
| Gly 1215 | - | expression tag |
| Arg 1216 | - | expression tag |
| Leu 1217 | - | expression tag |
| Val 1218 | - | expression tag |
| Pro 1219 | - | expression tag |
| Arg 1220 | - | expression tag |
| Gly 1221 | - | expression tag |
| Ser 1222 | - | expression tag |
| Pro 1223 | - | expression tag |
| Gly 1224 | - | expression tag |
| Ser 1225 | - | expression tag |
| Gly 1226 | - | expression tag |
| Tyr 1227 | - | expression tag |
| Ile 1228 | - | expression tag |
| Pro 1229 | - | expression tag |
| Glu 1230 | - | expression tag |
| Ala 1231 | - | expression tag |
| Pro 1232 | - | expression tag |
| Arg 1233 | - | expression tag |
| Asp 1234 | - | expression tag |
| Gly 1235 | - | expression tag |
| Gln 1236 | - | expression tag |
| Ala 1237 | - | expression tag |
| Tyr 1238 | - | expression tag |
| Val 1239 | - | expression tag |
| Arg 1240 | - | expression tag |
| Lys 1241 | - | expression tag |
| Asp 1242 | - | expression tag |
| Gly 1243 | - | expression tag |
| Glu 1244 | - | expression tag |
| Trp 1245 | - | expression tag |
| Val 1246 | - | expression tag |
| Leu 1247 | - | expression tag |
| Leu 1248 | - | expression tag |
| Ser 1249 | - | expression tag |
| Thr 1250 | - | expression tag |
| Phe 1251 | - | expression tag |
| Leu 1252 | - | expression tag |
| Gly 1253 | - | expression tag |
| His 1254 | - | expression tag |
| His 1255 | - | expression tag |
| His 1256 | - | expression tag |
| His 1257 | - | expression tag |
| His 1258 | - | expression tag |
| His 1259 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 514478.3 | |
| Branched | Number of molecules | 13 |
| Total formula weight | 5914.6 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 6636.2 | |
| All* | Total formula weight | 527029.1 |
