8XNF
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P) in complex with human ACE2
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A | Angiotensin-converting enzyme 2 | polymer | 603 | 69982.6 | 1 | UniProt (Q9BYF1) Pfam (PF01401) In PDB | Homo sapiens (human) | ACE-related carboxypeptidase,Angiotensin-converting enzyme homolog,ACEH,Metalloprotease MPROT15 |
2 | B, C, D | Spike glycoprotein | polymer | 1191 | 131772.4 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
3 | E | 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) | |||
4 | F, G, H, I, J | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 5 | In PDB GlyTouCan (G42666HT) | |||
5 | A | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
6 | C, D, A, B | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 33 | Chemie (NAG) |
Sequence modifications
A: 19 - 615 (UniProt: Q9BYF1)
B, C, D: 29 - 1146 (UniProt: P0DTC2)
PDB | External Database | Details |
---|---|---|
His 616 | - | expression tag |
His 617 | - | expression tag |
His 618 | - | expression tag |
His 619 | - | expression tag |
His 620 | - | expression tag |
His 621 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met 1 | - | initiating methionine |
Phe 2 | - | expression tag |
Val 3 | - | expression tag |
Phe 4 | - | expression tag |
Leu 5 | - | expression tag |
Val 6 | - | expression tag |
Leu 7 | - | expression tag |
Leu 8 | - | expression tag |
Pro 9 | - | expression tag |
Leu 10 | - | expression tag |
Val 11 | - | expression tag |
Ser 12 | - | expression tag |
Ser 13 | - | expression tag |
Gln 14 | - | expression tag |
Cys 15 | - | expression tag |
Val 16 | - | expression tag |
Met 17 | - | expression tag |
Pro 18 | - | expression tag |
Leu 19 | - | expression tag |
Phe 20 | - | expression tag |
Asn 21 | - | expression tag |
Leu 22 | - | expression tag |
Ile 23 | - | expression tag |
Thr 24 | - | expression tag |
Thr 25 | - | expression tag |
Thr 26 | - | expression tag |
Gln 27 | - | expression tag |
Ser 28 | - | expression tag |
Leu 51 | Ser 50 | variant |
- | His 69 | deletion |
- | Val 70 | deletion |
Phe 127 | Val 127 | variant |
Asp 143 | Gly 142 | variant |
- | Tyr 144 | deletion |
Ser 157 | Phe 157 | variant |
Gly 158 | Arg 158 | variant |
- | Asn 211 | deletion |
Ile 212 | Leu 212 | variant |
Gly 213 | Val 213 | variant |
Phe 216 | Leu 216 | variant |
Asn 245 | His 245 | variant |
Asp 264 | Ala 264 | variant |
Val 332 | Ile 332 | variant |
His 339 | Gly 339 | variant |
Thr 356 | Lys 356 | variant |
Phe 371 | Ser 371 | variant |
Pro 373 | Ser 373 | variant |
Phe 375 | Ser 375 | variant |
Ala 376 | Thr 376 | variant |
Lys 403 | Arg 403 | variant |
Asn 405 | Asp 405 | variant |
Ser 408 | Arg 408 | variant |
Asn 417 | Lys 417 | variant |
Lys 440 | Asn 440 | variant |
His 445 | Val 445 | variant |
Ser 446 | Gly 446 | variant |
Asp 450 | Asn 450 | variant |
Trp 452 | Leu 452 | variant |
Lys 460 | Asn 460 | variant |
Asn 477 | Ser 477 | variant |
Lys 478 | Thr 478 | variant |
Lys 481 | Asn 481 | variant |
- | Val 483 | deletion |
Lys 483 | Glu 484 | variant |
Pro 485 | Phe 486 | variant |
Arg 497 | Gln 498 | variant |
Tyr 500 | Asn 501 | variant |
His 504 | Tyr 505 | variant |
Lys 553 | Glu 554 | variant |
Val 569 | Ala 570 | variant |
Gly 613 | Asp 614 | variant |
Ser 620 | Pro 621 | variant |
Tyr 654 | His 655 | variant |
Val 669 | Ile 670 | variant |
Lys 678 | Asn 679 | variant |
Arg 680 | Pro 681 | variant |
Gly 681 | Arg 682 | engineered mutation |
Ser 682 | Arg 683 | engineered mutation |
Ser 684 | Arg 685 | engineered mutation |
Lys 763 | Asn 764 | variant |
Tyr 795 | Asp 796 | variant |
Pro 816 | Phe 817 | engineered mutation |
Pro 891 | Ala 892 | engineered mutation |
Pro 898 | Ala 899 | engineered mutation |
Phe 938 | Ser 939 | variant |
Pro 941 | Ala 942 | engineered mutation |
His 953 | Gln 954 | variant |
Lys 968 | Asn 969 | variant |
Pro 985 | Lys 986 | engineered mutation |
Pro 986 | Val 987 | engineered mutation |
Leu 1142 | Pro 1143 | variant |
Gly 1147 | - | expression tag |
Gly 1148 | - | expression tag |
Gly 1149 | - | expression tag |
Ser 1150 | - | expression tag |
Gly 1151 | - | expression tag |
Gly 1152 | - | expression tag |
Gly 1153 | - | expression tag |
Ser 1154 | - | expression tag |
Gly 1155 | - | expression tag |
Tyr 1156 | - | expression tag |
Ile 1157 | - | expression tag |
Pro 1158 | - | expression tag |
Glu 1159 | - | expression tag |
Ala 1160 | - | expression tag |
Pro 1161 | - | expression tag |
Arg 1162 | - | expression tag |
Asp 1163 | - | expression tag |
Gly 1164 | - | expression tag |
Gln 1165 | - | expression tag |
Ala 1166 | - | expression tag |
Tyr 1167 | - | expression tag |
Val 1168 | - | expression tag |
Arg 1169 | - | expression tag |
Lys 1170 | - | expression tag |
Asp 1171 | - | expression tag |
Gly 1172 | - | expression tag |
Glu 1173 | - | expression tag |
Trp 1174 | - | expression tag |
Val 1175 | - | expression tag |
Leu 1176 | - | expression tag |
Leu 1177 | - | expression tag |
Ser 1178 | - | expression tag |
Thr 1179 | - | expression tag |
Phe 1180 | - | expression tag |
Leu 1181 | - | expression tag |
Gly 1182 | - | expression tag |
Gly 1183 | - | expression tag |
Gly 1184 | - | expression tag |
Ser 1185 | - | expression tag |
Ala 1186 | - | expression tag |
Trp 1187 | - | expression tag |
Ser 1188 | - | expression tag |
His 1189 | - | expression tag |
Pro 1190 | - | expression tag |
Gln 1191 | - | expression tag |
Phe 1192 | - | expression tag |
Glu 1193 | - | expression tag |
Lys 1194 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 4 |
Total formula weight | 465299.8 | |
Branched | Number of molecules | 6 |
Total formula weight | 2708.5 | |
Non-Polymers* | Number of molecules | 34 |
Total formula weight | 7365.3 | |
All* | Total formula weight | 475373.6 |