8JAM
Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (B) | Spike glycoprotein | polymer | 1274 | 141600.3 | 1 | UniProt (A0A7D8AJB5) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) UniProt (by SIFTS) (A0A6V7ALX9) | Severe acute respiratory syndrome-related coronavirus | S glycoprotein,E2,Peplomer protein |
| 2 | B (H) | H chain of W328-6H2 | polymer | 107 | 11654.1 | 1 | Homo sapiens | ||
| 3 | C (L) | L chain of W328-6H2 | polymer | 112 | 12276.7 | 1 | Homo sapiens | ||
| 4 | D (A) | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | branched | 570.5 | 1 | In PDB GlyTouCan (G21290RB) | |||
| 5 | E, F (B) | 2-acetamido-2-deoxy-beta-D-glucopyranose | non-polymer | 221.2 | 2 | Chemie (NAG) |
Sequence modifications
B: -324 - 880 (UniProt: A0A7D8AJB5)
| PDB | External Database | Details |
|---|---|---|
| Val -258 | Ala 67 | conflict |
| - | His 69 | deletion |
| - | Val 70 | deletion |
| Ile -232 | Thr 95 | conflict |
| Asp -185 | Gly 142 | conflict |
| - | Val 143 | deletion |
| - | Tyr 144 | deletion |
| - | Asn 210 | deletion |
| Ile -119 | Leu 211 | conflict |
| Glu -116 | - | insertion |
| Pro -115 | - | insertion |
| Glu -114 | - | insertion |
| Asp 11 | Gly 338 | conflict |
| Leu 43 | Ser 370 | conflict |
| Pro 45 | Ser 372 | conflict |
| Phe 47 | Ser 374 | conflict |
| Asn 89 | Lys 416 | conflict |
| Lys 112 | Asn 439 | conflict |
| Ser 118 | Gly 445 | conflict |
| Asn 149 | Ser 476 | conflict |
| Lys 150 | Thr 477 | conflict |
| Ala 156 | Glu 483 | conflict |
| Arg 165 | Gln 492 | conflict |
| Ser 168 | Gly 495 | conflict |
| Arg 170 | Gln 497 | conflict |
| Tyr 173 | Asn 500 | conflict |
| His 177 | Tyr 504 | conflict |
| Lys 219 | Thr 546 | conflict |
| Tyr 327 | His 654 | conflict |
| Lys 351 | Asn 678 | conflict |
| His 353 | Pro 680 | conflict |
| Ser 354 | Arg 681 | conflict |
| Gly 355 | Arg 682 | conflict |
| Gly 357 | Arg 684 | conflict |
| Cys 379 | Tyr 706 | conflict |
| Lys 436 | Asn 763 | conflict |
| Tyr 468 | Asp 795 | conflict |
| Pro 489 | Phe 816 | conflict |
| Lys 528 | Asn 855 | conflict |
| Cys 555 | Thr 882 | conflict |
| Pro 564 | Ala 891 | conflict |
| Pro 571 | Ala 898 | conflict |
| Pro 614 | Ala 941 | conflict |
| His 626 | Gln 953 | conflict |
| Lys 641 | Asn 968 | conflict |
| Phe 653 | Leu 980 | conflict |
| Pro 659 | Val 986 | conflict |
| Gly 881 | - | expression tag |
| Ser 882 | - | expression tag |
| Gly 883 | - | expression tag |
| Tyr 884 | - | expression tag |
| Ile 885 | - | expression tag |
| Pro 886 | - | expression tag |
| Glu 887 | - | expression tag |
| Ala 888 | - | expression tag |
| Pro 889 | - | expression tag |
| Arg 890 | - | expression tag |
| Asp 891 | - | expression tag |
| Gly 892 | - | expression tag |
| Gln 893 | - | expression tag |
| Ala 894 | - | expression tag |
| Tyr 895 | - | expression tag |
| Val 896 | - | expression tag |
| Arg 897 | - | expression tag |
| Lys 898 | - | expression tag |
| Asp 899 | - | expression tag |
| Gly 900 | - | expression tag |
| Glu 901 | - | expression tag |
| Trp 902 | - | expression tag |
| Val 903 | - | expression tag |
| Leu 904 | - | expression tag |
| Leu 905 | - | expression tag |
| Ser 906 | - | expression tag |
| Thr 907 | - | expression tag |
| Phe 908 | - | expression tag |
| Leu 909 | - | expression tag |
| Gly 910 | - | expression tag |
| Arg 911 | - | expression tag |
| Ser 912 | - | expression tag |
| Leu 913 | - | expression tag |
| Glu 914 | - | expression tag |
| Val 915 | - | expression tag |
| Leu 916 | - | expression tag |
| Phe 917 | - | expression tag |
| Gln 918 | - | expression tag |
| Gly 919 | - | expression tag |
| Pro 920 | - | expression tag |
| Gly 921 | - | expression tag |
| Ser 922 | - | expression tag |
| Gly 923 | - | expression tag |
| Gly 924 | - | expression tag |
| Leu 925 | - | expression tag |
| Asn 926 | - | expression tag |
| Asp 927 | - | expression tag |
| Ile 928 | - | expression tag |
| Phe 929 | - | expression tag |
| Glu 930 | - | expression tag |
| Ala 931 | - | expression tag |
| Gln 932 | - | expression tag |
| Lys 933 | - | expression tag |
| Ile 934 | - | expression tag |
| Glu 935 | - | expression tag |
| Trp 936 | - | expression tag |
| His 937 | - | expression tag |
| Glu 938 | - | expression tag |
| Gly 939 | - | expression tag |
| Ser 940 | - | expression tag |
| Gly 941 | - | expression tag |
| His 942 | - | expression tag |
| His 943 | - | expression tag |
| His 944 | - | expression tag |
| His 945 | - | expression tag |
| His 946 | - | expression tag |
| His 947 | - | expression tag |
| His 948 | - | expression tag |
| His 949 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 165531.1 | |
| Branched | Number of molecules | 1 |
| Total formula weight | 570.5 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 442.4 | |
| All* | Total formula weight | 166544.1 |
