8K5H
Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
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 (B, A, C) | Spike glycoprotein | polymer | 1200 | 133229.9 | 3 | UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2) | S glycoprotein,E2,Peplomer protein |
| 2 | D (H) | UT28K-RD Fab heavy chain | polymer | 252 | 27100.4 | 1 | Homo sapiens | ||
| 3 | E (L) | UT28K-RD Fab light chain | polymer | 235 | 25728.7 | 1 | Homo sapiens | ||
| 4 | F, G, H, I, J... (D, E, F, G, I...) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 424.4 | 8 | In PDB GlyTouCan (G42666HT) | |||
| 5 | AA, BA, CA, DA, EA... (A, C, B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 34 | Chemie (NAG) |
Sequence modifications
B, A, C: 12 - 1207 (UniProt: P0DTC2)
| PDB | External Database | Details |
|---|---|---|
| Gly 10 | - | expression tag |
| Thr 11 | - | expression tag |
| Val 67 | Ala 67 | variant |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile 93 | Thr 95 | variant |
| - | Gly 142 | deletion |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| Asp 140 | Tyr 145 | variant |
| - | Asn 211 | deletion |
| Ile 206 | Leu 212 | variant |
| 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 |
| Gly 679 | Arg 682 | engineered mutation |
| Ser 680 | Arg 683 | engineered mutation |
| Gly 682 | Arg 685 | engineered mutation |
| Lys 761 | Asn 764 | variant |
| Tyr 793 | Asp 796 | variant |
| Pro 814 | Phe 817 | engineered mutation |
| Lys 853 | Asn 856 | conflict |
| Pro 889 | Ala 892 | engineered mutation |
| Pro 896 | Ala 899 | engineered mutation |
| Pro 939 | Ala 942 | engineered mutation |
| His 951 | Gln 954 | variant |
| Lys 966 | Asn 969 | variant |
| Phe 978 | Leu 981 | variant |
| Pro 983 | Lys 986 | engineered mutation |
| Pro 984 | Val 987 | engineered mutation |
| Ala 1208 | - | expression tag |
| Ser 1209 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 452518.9 | |
| Branched | Number of molecules | 8 |
| Total formula weight | 3395.2 | |
| Non-Polymers* | Number of molecules | 34 |
| Total formula weight | 7521.1 | |
| All* | Total formula weight | 463435.2 |
