8GTQ
cryo-EM structure of Omicron BA.5 S protein in complex with S2L20
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 | 1271 | 141326.8 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, F, H (H, I, J) | heavy chain of S2L20 | polymer | 121 | 13454.0 | 3 | Homo sapiens | ||
| 3 | E, G, I (L, M, N) | light chain of S2L20 | polymer | 107 | 11829.1 | 3 | Homo sapiens | ||
| 4 | J, Q, X (D, Q, X) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 627.6 | 3 | In PDB GlyTouCan (G47362BJ) | |||
| 5 | AA, BA, CA, DA, K... (a, b, c, d, E...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 18 | In PDB GlyTouCan (G42666HT) | |||
| 6 | AB, BB, CB, DB, EA... (C, A, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 30 | Chemie (NAG) |
Sequence modifications
A, B, C: 1 - 1273 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Ile 19 | Thr 19 | variant |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Asp 142 | Gly 142 | variant |
| Gly 213 | Val 213 | variant |
| Asp 339 | Gly 339 | variant |
| Phe 371 | Ser 371 | variant |
| Pro 373 | Ser 373 | variant |
| Phe 375 | Ser 375 | variant |
| Ala 376 | Thr 376 | variant |
| Asn 405 | Asp 405 | variant |
| Ser 408 | Arg 408 | variant |
| Asn 417 | Lys 417 | variant |
| Lys 440 | Asn 440 | variant |
| Arg 452 | Leu 452 | variant |
| Asn 477 | Ser 477 | variant |
| Lys 478 | Thr 478 | variant |
| Ala 484 | Glu 484 | variant |
| Val 486 | Phe 486 | variant |
| Arg 498 | Gln 498 | variant |
| Tyr 501 | Asn 501 | variant |
| His 505 | Tyr 505 | variant |
| Gly 614 | Asp 614 | variant |
| Tyr 655 | His 655 | variant |
| Lys 679 | Asn 679 | variant |
| His 681 | Pro 681 | variant |
| Lys 764 | Asn 764 | variant |
| Tyr 796 | Asp 796 | variant |
| Pro 817 | Phe 817 | variant |
| Pro 892 | Ala 892 | variant |
| Pro 899 | Ala 899 | variant |
| Pro 942 | Ala 942 | variant |
| His 954 | Gln 954 | variant |
| Lys 969 | Asn 969 | variant |
| Pro 986 | Lys 986 | variant |
| Pro 987 | Val 987 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 9 |
| Total formula weight | 499829.7 | |
| Branched | Number of molecules | 21 |
| Total formula weight | 9522.0 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 6636.2 | |
| All* | Total formula weight | 515988.0 |
