7WE9
SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv289
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, F | Spike glycoprotein | polymer | 1270 | 141456.1 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | C, H, I | The heavy chain of Fab XGv289 | polymer | 120 | 13098.6 | 3 | Homo sapiens | ||
| 3 | J, K, L | The light chain of Fab XGv289 | polymer | 111 | 11586.7 | 3 | Homo sapiens | ||
| 4 | a, D, E, G, M... | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 15 | In PDB GlyTouCan (G42666HT) | |||
| 5 | b, c, O, V, W | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 586.5 | 5 | In PDB GlyTouCan (G15407YE) | |||
| 6 | F, A, B | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 27 | Chemie (NAG) |
Sequence modifications
A, B, F: 1 - 1270 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Val 67 | Ala 67 | variant |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 93 | Thr 95 | variant |
| Asp 140 | Gly 142 | variant |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| - | Tyr 145 | deletion |
| - | Asn 211 | deletion |
| Glu 209 | - | insertion |
| Pro 210 | - | insertion |
| Glu 211 | - | insertion |
| Asp 336 | Gly 339 | variant |
| Leu 368 | Ser 371 | variant |
| Pro 370 | Ser 373 | variant |
| Phe 372 | Ser 375 | variant |
| Asn 414 | Lys 417 | variant |
| Lys 437 | Asn 440 | variant |
| Ser 443 | Gly 446 | variant |
| Asn 474 | Ser 477 | variant |
| Lys 475 | Thr 478 | variant |
| Ala 481 | Glu 484 | variant |
| Arg 490 | Gln 493 | variant |
| Ser 493 | Gly 496 | variant |
| Arg 495 | Gln 498 | variant |
| Tyr 498 | Asn 501 | variant |
| His 502 | Tyr 505 | variant |
| Lys 544 | Thr 547 | variant |
| Gly 611 | Asp 614 | variant |
| Tyr 652 | His 655 | variant |
| Lys 676 | Asn 679 | variant |
| His 678 | Pro 681 | variant |
| Lys 761 | Asn 764 | variant |
| Tyr 793 | Asp 796 | variant |
| Lys 853 | Asn 856 | variant |
| His 951 | Gln 954 | variant |
| Lys 966 | Asn 969 | variant |
| Phe 978 | Leu 981 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 9 |
| Total formula weight | 498424.1 | |
| Branched | Number of molecules | 20 |
| Total formula weight | 9298.7 | |
| Non-Polymers* | Number of molecules | 27 |
| Total formula weight | 5972.6 | |
| All* | Total formula weight | 513695.5 |
