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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8JAM

Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(B)		Spike glycoproteinpolymer1274141600.31UniProt (A0A7D8AJB5)
Pfam (PF16451)
Pfam (PF09408)
Pfam (PF19209)
Pfam (PF01601)
UniProt (by SIFTS) (A0A6V7ALX9)		Severe acute respiratory syndrome-related coronavirusS glycoprotein,E2,Peplomer protein
2B
(H)		H chain of W328-6H2polymer10711654.11Homo sapiens
3C
(L)		L chain of W328-6H2polymer11212276.71Homo sapiens
4D
(A)		2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranosebranched570.51In PDB
GlyTouCan (G21290RB)
5E, F
(B)		2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.22Chemie (NAG)
Sequence modifications
B: -324 - 880 (UniProt: A0A7D8AJB5)
PDBExternal DatabaseDetails
Val -258Ala 67conflict
-His 69deletion
-Val 70deletion
Ile -232Thr 95conflict
Asp -185Gly 142conflict
-Val 143deletion
-Tyr 144deletion
-Asn 210deletion
Ile -119Leu 211conflict
Glu -116-insertion
Pro -115-insertion
Glu -114-insertion
Asp 11Gly 338conflict
Leu 43Ser 370conflict
Pro 45Ser 372conflict
Phe 47Ser 374conflict
Asn 89Lys 416conflict
Lys 112Asn 439conflict
Ser 118Gly 445conflict
Asn 149Ser 476conflict
Lys 150Thr 477conflict
Ala 156Glu 483conflict
Arg 165Gln 492conflict
Ser 168Gly 495conflict
Arg 170Gln 497conflict
Tyr 173Asn 500conflict
His 177Tyr 504conflict
Lys 219Thr 546conflict
Tyr 327His 654conflict
Lys 351Asn 678conflict
His 353Pro 680conflict
Ser 354Arg 681conflict
Gly 355Arg 682conflict
Gly 357Arg 684conflict
Cys 379Tyr 706conflict
Lys 436Asn 763conflict
Tyr 468Asp 795conflict
Pro 489Phe 816conflict
Lys 528Asn 855conflict
Cys 555Thr 882conflict
Pro 564Ala 891conflict
Pro 571Ala 898conflict
Pro 614Ala 941conflict
His 626Gln 953conflict
Lys 641Asn 968conflict
Phe 653Leu 980conflict
Pro 659Val 986conflict
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
PolymersNumber of chains3
Total formula weight165531.1
BranchedNumber of molecules1
Total formula weight570.5
Non-Polymers*Number of molecules2
Total formula weight442.4
All*Total formula weight166544.1
*Water molecules are not included.

239149

PDB entries from 2025-07-23

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