7ZSS
cryo-EM structure of D614 spike in complex with de novo designed binder
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 | 1146 | 126639.5 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, E, F (D, P, h) | de novo designed binder | polymer | 79 | 8829.9 | 3 | UniProt (Q9VKJ9) Pfam (PF21528) | Drosophila melanogaster (fruit fly) | |
| 3 | G, H, I, J, K... (E, F, G, H, I...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 7 | In PDB GlyTouCan (G42666HT) | |||
| 4 | AA, BA, CA, DA, EA... (B, C, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 32 | Chemie (NAG) |
Sequence modifications
A, B, C: 1 - 1146 (UniProt: P0DTC2)
D, P, h: 1 - 65 (UniProt: Q9VKJ9)
| PDB | External Database | Details |
|---|---|---|
| Gly 614 | Asp 614 | variant |
| Gly 682 | Arg 682 | engineered mutation |
| Ser 683 | Arg 683 | engineered mutation |
| Ser 685 | Arg 685 | engineered mutation |
| Pro 986 | Lys 986 | engineered mutation |
| Pro 987 | Val 987 | engineered mutation |
| 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 | 6 |
| Total formula weight | 406408.2 | |
| Branched | Number of molecules | 7 |
| Total formula weight | 2970.8 | |
| Non-Polymers* | Number of molecules | 32 |
| Total formula weight | 7078.7 | |
| All* | Total formula weight | 416457.7 |
