8HC2
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)
This is a non-PDB format compatible entry.
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | B, C, A | Spike glycoprotein | polymer | 1240 | 138036.2 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
2 | L | Light chain of YB9-258 Fab | polymer | 215 | 23177.8 | 1 | Homo sapiens | ||
3 | H | Heavy chain of YB9-258 Fab | polymer | 220 | 23126.9 | 1 | Homo sapiens | ||
4 | D, E, F, G, I... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 12 | In PDB GlyTouCan (G42666HT) | |||
5 | B, C, A | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 30 | Chemie (NAG) |
Sequence modifications
B, C, A: 14 - 1211 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
Val 67 | Ala 67 | variant |
- | His 69 | deletion |
- | Val 70 | deletion |
Ile 95 | Thr 95 | variant |
Asp 142 | Gly 142 | variant |
- | Val 143 | deletion |
- | Tyr 144 | deletion |
- | Tyr 145 | deletion |
Ile 210 | Leu 212 | variant |
Glu 210 | - | insertion |
Pro 210 | - | insertion |
Glu 210 | - | insertion |
Asp 339 | Gly 339 | variant |
Leu 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
Ser 446 | Gly 446 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Ala 484 | Glu 484 | variant |
Arg 493 | Gln 493 | variant |
Ser 496 | Gly 496 | variant |
Arg 498 | Gln 498 | variant |
Tyr 501 | Asn 501 | variant |
His 505 | Tyr 505 | variant |
Lys 547 | Thr 547 | variant |
Gly 614 | Asp 614 | variant |
Tyr 655 | His 655 | variant |
Lys 683 | Asn 679 | variant |
- | Pro 681 | deletion |
- | Arg 682 | deletion |
- | Arg 683 | deletion |
- | Ala 684 | deletion |
Lys 764 | Asn 764 | variant |
Tyr 796 | Asp 796 | variant |
Pro 817 | Phe 817 | engineered mutation |
Lys 856 | Asn 856 | variant |
Pro 892 | Ala 892 | engineered mutation |
Pro 899 | Ala 899 | engineered mutation |
Pro 942 | Ala 942 | engineered mutation |
His 954 | Gln 954 | variant |
Lys 969 | Asn 969 | variant |
Phe 981 | Leu 981 | variant |
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 |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 5 |
Total formula weight | 460413.2 | |
Branched | Number of molecules | 12 |
Total formula weight | 5092.8 | |
Non-Polymers* | Number of molecules | 30 |
Total formula weight | 6636.2 | |
All* | Total formula weight | 472142.3 |