7XST
Cryo-EM structure of SARS-CoV-2 Omicron spike glycoprotein in complex with three F61 Fab and three D2 Fab
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 | 1210 | 134628.8 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, H, L (L, H, D) | F61 heavy chain | polymer | 117 | 12993.5 | 3 | Homo sapiens | ||
| 3 | E, I, M (M, I, E) | F61 light chain | polymer | 110 | 11472.6 | 3 | Homo sapiens | ||
| 4 | F, J, N (N, J, F) | D2 heavy chain | polymer | 123 | 13406.8 | 3 | Homo sapiens | ||
| 5 | G, K, O (O, K, G) | D2 light chain | polymer | 110 | 11468.7 | 3 | Homo sapiens | ||
| 6 | AA, BA, CA, DA, EA... (B, C, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 31 | Chemie (NAG) |
Sequence modifications
A, B, C: 1 - 1213 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 67 | Ala 67 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 95 | Thr 95 | conflict |
| Asp 142 | Gly 142 | conflict |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| - | Tyr 145 | deletion |
| Ile 210 | - | insertion |
| Val 210 | - | insertion |
| Arg 210 | Asn 211 | conflict |
| Glu 210 | Leu 212 | conflict |
| Pro 210 | Val 213 | conflict |
| Glu 210 | Arg 214 | conflict |
| Asp 339 | Gly 339 | conflict |
| Leu 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Asn 417 | Lys 417 | conflict |
| Lys 440 | Asn 440 | conflict |
| Ser 446 | Gly 446 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Arg 493 | Gln 493 | conflict |
| Ser 496 | Gly 496 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Lys 547 | Thr 547 | conflict |
| Gly 614 | Asp 614 | conflict |
| Tyr 655 | His 655 | conflict |
| Lys 679 | Asn 679 | conflict |
| His 681 | Pro 681 | conflict |
| Gly 682 | Arg 682 | conflict |
| Ser 683 | Arg 683 | conflict |
| Ser 685 | Arg 685 | conflict |
| Lys 764 | Asn 764 | conflict |
| Tyr 796 | Asp 796 | conflict |
| Pro 817 | Phe 817 | engineered mutation |
| Lys 856 | Asn 856 | conflict |
| Pro 892 | Ala 892 | engineered mutation |
| Pro 899 | Ala 899 | engineered mutation |
| Pro 942 | Ala 942 | engineered mutation |
| His 954 | Gln 954 | conflict |
| Lys 969 | Asn 969 | conflict |
| Phe 981 | Leu 981 | conflict |
| Pro 986 | Lys 986 | engineered mutation |
| Pro 987 | Val 987 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 15 |
| Total formula weight | 551911.4 | |
| Non-Polymers* | Number of molecules | 31 |
| Total formula weight | 6857.4 | |
| All* | Total formula weight | 558768.8 |
