7XOD

SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab Bound

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	Spike glycoprotein	polymer	1270	141065.4	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	X, U, R	Heavy chain of JMB2002 Fab	polymer	229	24150.0	3		Homo sapiens
3	Y, V, S	Light chain of JMB2002 Fab	polymer	214	23331.9	3		Homo sapiens
4	Z, W, T	Nanobody	polymer	124	13521.8	3		Lama glama
5	D, E	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
6	B, C, A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	35	Chemie (NAG)

Sequence modifications

A, B, C: 4 - 1273 (UniProt: P0DTC2)

PDB	External Database	Details
Ile 22	Thr 19	variant
-	Leu 24	deletion
-	Pro 25	deletion
-	Pro 26	deletion
Ser 27	Ala 27	variant
Asp 142	Gly 142	variant
Gly 213	Val 213	variant
Asp 339	Gly 339	variant
Phe 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Ala 376	Thr 376	variant
Asn 405	Asp 405	variant
Ser 408	Arg 408	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Arg 493	Gln 493	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Gly 614	Asp 614	variant
Tyr 655	His 655	variant
Lys 679	Asn 679	variant
His 681	Pro 681	variant
Gly 682	Arg 682	engineered mutation
Ser 683	Arg 683	engineered mutation
Ser 685	Arg 685	engineered mutation
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	engineered mutation
Pro 892	Ala 892	engineered mutation
Pro 899	Ala 899	engineered mutation
Pro 942	Ala 942	engineered mutation
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Pro 986	Lys 986	engineered mutation
Pro 987	Val 987	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	606207.4
Branched	Number of molecules	2
	Total formula weight	848.8
Non-Polymers*	Number of molecules	35
	Total formula weight	7742.3
All*	Total formula weight	614798.5

*Water molecules are not included.