9ELG
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike RBD and NTD (local refinement of RBD and NTD)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Spike protein S1 | polymer | 285 | 32357.5 | 1 | UniProt (P0DTC2) Pfam (PF16451) | Severe acute respiratory syndrome coronavirus 2 | S glycoprotein,E2,Peplomer protein |
| 2 | B (C) | Spike protein S1 | polymer | 272 | 30795.9 | 1 | UniProt (P0DTC2) Pfam (PF09408) Pfam (PF19209) | Severe acute respiratory syndrome coronavirus 2 | |
| 3 | C (B) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 1 | In PDB GlyTouCan (G42666HT) | |||
| 4 | D, E, F, G, H... (A, C) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 9 | Chemie (NAG) |
Sequence modifications
A: 4 - 289 (UniProt: P0DTC2)
C: 318 - 590 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Ile 22 | Thr 19 | variant |
| Thr 24 | Arg 21 | conflict |
| - | Leu 24 | deletion |
| - | Pro 25 | deletion |
| - | Pro 26 | deletion |
| Ser 27 | Ala 27 | conflict |
| - | Ser 31 | deletion |
| Leu 50 | Ser 50 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Phe 125 | Val 127 | conflict |
| Asp 140 | Gly 142 | variant |
| - | Tyr 145 | deletion |
| Ser 154 | Phe 157 | conflict |
| Gly 155 | Arg 158 | conflict |
| - | Asn 211 | deletion |
| Ile 208 | Leu 212 | conflict |
| Gly 209 | Val 213 | variant |
| Phe 212 | Leu 216 | conflict |
| Asn 241 | His 245 | conflict |
| Asp 260 | Ala 264 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Val 332 | Ile 332 | conflict |
| His 339 | Gly 339 | variant |
| Thr 356 | Lys 356 | conflict |
| Phe 371 | Ser 371 | variant |
| Pro 373 | Ser 373 | variant |
| Phe 375 | Ser 375 | variant |
| Ala 376 | Thr 376 | variant |
| Lys 403 | Arg 403 | conflict |
| Asn 405 | Asp 405 | variant |
| Ser 408 | Arg 408 | variant |
| Asn 417 | Lys 417 | variant |
| Lys 440 | Asn 440 | variant |
| His 445 | Val 445 | conflict |
| Ser 446 | Gly 446 | variant |
| Asp 450 | Asn 450 | conflict |
| Trp 452 | Leu 452 | conflict |
| Ser 455 | Leu 455 | conflict |
| Leu 456 | Phe 456 | variant |
| Lys 460 | Asn 460 | variant |
| Asn 477 | Ser 477 | variant |
| Lys 478 | Thr 478 | variant |
| Lys 481 | Asn 481 | conflict |
| - | Val 483 | deletion |
| Lys 484 | Glu 484 | variant |
| Pro 486 | Phe 486 | variant |
| Glu 493 | Gln 493 | conflict |
| Arg 498 | Gln 498 | variant |
| Tyr 501 | Asn 501 | variant |
| His 505 | Tyr 505 | variant |
| Lys 554 | Glu 554 | conflict |
| Val 570 | Ala 570 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total formula weight | 63153.4 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 424.4 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 1990.9 | |
| All* | Total formula weight | 65568.7 |
