8VKP
Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A | Spike protein S1 | polymer | 201 | 22580.5 | 1 | UniProt (P0DTC2) Pfam (PF09408) In PDB | Severe acute respiratory syndrome coronavirus 2 | |
| 2 | D | Processed angiotensin-converting enzyme 2 | polymer | 606 | 70387.0 | 1 | UniProt (Q9BYF1) Pfam (PF01401) In PDB | Homo sapiens (human) | |
| 3 | B, C | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
| 4 | A, D | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 5 | Chemie (NAG) |
Sequence modifications
A: null - 527 (UniProt: P0DTC2)
D: 18 - 615 (UniProt: Q9BYF1)
| PDB | External Database | Details |
|---|---|---|
| - | Val 327 | deletion |
| - | Arg 328 | deletion |
| - | Phe 329 | deletion |
| His 339 | Gly 339 | conflict |
| Thr 346 | Arg 346 | conflict |
| Ile 368 | Leu 368 | conflict |
| Phe 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Ala 376 | Thr 376 | conflict |
| Asn 405 | Asp 405 | conflict |
| Ser 408 | Arg 408 | conflict |
| Asn 417 | Lys 417 | conflict |
| Lys 440 | Asn 440 | conflict |
| Pro 445 | Val 445 | conflict |
| Ser 446 | Gly 446 | conflict |
| Lys 460 | Asn 460 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Pro 486 | Phe 486 | conflict |
| Ser 490 | Phe 490 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Lys 528 | - | expression tag |
| Lys 529 | - | expression tag |
| Ser 530 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| His 616 | - | expression tag |
| His 617 | - | expression tag |
| His 618 | - | expression tag |
| His 619 | - | expression tag |
| His 620 | - | expression tag |
| His 621 | - | expression tag |
| His 622 | - | expression tag |
| His 623 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 92967.5 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 848.8 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 1106.0 | |
| All* | Total formula weight | 94922.4 |
