7ZSD
cryo-EM structure of omicron spike in complex with de novo designed binder, local
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (M) | Spike glycoprotein | polymer | 196 | 22280.2 | 1 | UniProt (P0DTC2) Pfam (PF09408) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | B (P) | de novo designed binder | polymer | 79 | 8829.9 | 1 | UniProt (Q9VKJ9) Pfam (PF21528) | Drosophila melanogaster (fruit fly) | |
| 3 | C (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) |
Sequence modifications
M: 332 - 527 (UniProt: P0DTC2)
P: 1 - 65 (UniProt: Q9VKJ9)
| PDB | External Database | Details |
|---|---|---|
| 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 | engineered mutation |
| Ser 496 | Gly 496 | variant |
| Arg 498 | Gln 498 | variant |
| Tyr 501 | Asn 501 | variant |
| His 505 | Tyr 505 | variant |
| PDB | External Database | Details |
|---|---|---|
| Glu -5 | - | expression tag |
| Thr -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Ala -2 | - | expression tag |
| Ser -1 | - | expression tag |
| Ser 0 | - | expression tag |
| Gln 12 | Glu 370 | engineered mutation |
| Phe 13 | Lys 371 | engineered mutation |
| His 15 | Gln 373 | engineered mutation |
| Gly 16 | Ser 374 | engineered mutation |
| Gln 17 | Val 375 | engineered mutation |
| Val 18 | Glu 376 | engineered mutation |
| Arg 20 | Ala 378 | engineered mutation |
| Ala 22 | Lys 380 | engineered mutation |
| Leu 23 | Ala 381 | engineered mutation |
| Gly 66 | - | expression tag |
| Ser 67 | - | expression tag |
| Glu 68 | - | expression tag |
| Asn 69 | - | expression tag |
| Leu 70 | - | expression tag |
| Tyr 71 | - | expression tag |
| Phe 72 | - | expression tag |
| Gln 73 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 31110.1 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 424.4 | |
| All* | Total formula weight | 31534.5 |
