7XDB
Cryo-EM structure of SARS-CoV-2 Omicron Spike protein in complex with BA7208 fab
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E, H (E, F, H) | BA7208 fab | polymer | 106 | 11628.9 | 3 | Homo sapiens | ||
| 2 | B, F, G (A, C, B) | Spike glycoprotein | polymer | 1116 | 124036.9 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 3 | C, D, I (D, G, I) | BA7208 fab | polymer | 118 | 13181.8 | 3 | Homo sapiens | ||
| 4 | J, K, L, M, N... (O, S, U, Z, d...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 11 | In PDB GlyTouCan (G42666HT) | |||
| 5 | AA, BA, CA, DA, EA... (C, B, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 16 | Chemie (NAG) |
Sequence modifications
A, C, B: 29 - 1144 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 70 | Ala 67 | variant |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 96 | Thr 95 | variant |
| Asp 143 | Gly 142 | variant |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| Ile 209 | Leu 212 | variant |
| Glu 212 | - | insertion |
| Pro 213 | - | insertion |
| Glu 214 | - | 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 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 |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 9 |
| Total formula weight | 446542.8 | |
| Branched | Number of molecules | 11 |
| Total formula weight | 4668.4 | |
| Non-Polymers* | Number of molecules | 16 |
| Total formula weight | 3539.3 | |
| All* | Total formula weight | 454750.5 |
