8KHC
SARS-CoV-2 Omicron spike in complex with 5817 Fab
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 | 1120 | 124547.5 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | D, F (F, H) | Heavy chain of 5817 Fab | polymer | 125 | 13387.0 | 2 | Homo sapiens | ||
| 3 | E, G (G, J) | Light chain of 5817 Fab | polymer | 108 | 11470.5 | 2 | Homo sapiens | ||
| 4 | H, I (D, E) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 2 | In PDB GlyTouCan (G42666HT) | |||
| 5 | AA, BA, CA, DA, EA... (B, C, A) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 36 | Chemie (NAG) | |||
| 6 | TA, UA, VA, WA, XA... (A, B, F, G, H...) | water | water | 18.0 | 58 | Chemie (HOH) |
Sequence modifications
A, B, C: 27 - 1149 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 67 | Ala 67 | conflict |
| Ile 95 | Thr 95 | conflict |
| Asp 142 | Gly 142 | conflict |
| Asp 156 | Glu 156 | conflict |
| Asp 339 | Gly 339 | conflict |
| Leu 371 | Ser 371 | conflict |
| Pro 373 | Ser 373 | conflict |
| Phe 375 | Ser 375 | conflict |
| Asn 417 | Lys 417 | conflict |
| Lys 440 | Asn 440 | conflict |
| Ser 446 | Gly 446 | conflict |
| Asn 477 | Ser 477 | conflict |
| Lys 478 | Thr 478 | conflict |
| Ala 484 | Glu 484 | conflict |
| Arg 493 | Gln 493 | conflict |
| Ser 496 | Gly 496 | conflict |
| Arg 498 | Gln 498 | conflict |
| Tyr 501 | Asn 501 | conflict |
| His 505 | Tyr 505 | conflict |
| Lys 550 | Thr 547 | conflict |
| Gly 617 | Asp 614 | conflict |
| Tyr 658 | His 655 | conflict |
| Lys 767 | Asn 764 | conflict |
| Tyr 799 | Asp 796 | conflict |
| Lys 859 | Asn 856 | conflict |
| His 957 | Gln 954 | conflict |
| Lys 972 | Asn 969 | conflict |
| Phe 984 | Leu 981 | conflict |
| Pro 989 | Lys 986 | conflict |
| Pro 990 | Val 987 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 7 |
| Total formula weight | 423357.6 | |
| Branched | Number of molecules | 2 |
| Total formula weight | 848.8 | |
| Non-Polymers* | Number of molecules | 36 |
| Total formula weight | 7963.5 | |
| All* | Total formula weight | 432169.9 |
