7WPE

SARS-CoV-2 Omicron Variant S Trimer complexed with two JMB2002 Fab

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	1205	133912.0	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	JMB2002 Fab heavy chain	polymer	237	25218.2	2		Mus musculus
3	Y, V	JMB2002 Fab light chian	polymer	215	23388.9	2		Mus musculus
4	Z, W	Anti-Fab nanobody	polymer	133	14645.9	2		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	36	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1211 (UniProt: P0DTC2)

PDB	External Database	Details
Val 67	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
Ile 95	Thr 95	variant
Asp 142	Gly 142	variant
-	Val 143	deletion
-	Tyr 144	deletion
-	Tyr 145	deletion
-	Asn 211	deletion
Ile 212	Leu 212	variant
Glu 215	-	insertion
Pro 216	-	insertion
Glu 217	-	insertion
Asp 342	Gly 339	variant
Leu 374	Ser 371	variant
Pro 376	Ser 373	variant
Phe 378	Ser 375	variant
Asn 420	Lys 417	variant
Lys 443	Asn 440	variant
Ser 449	Gly 446	variant
Asn 480	Ser 477	variant
Lys 481	Thr 478	variant
Ala 487	Glu 484	variant
Arg 496	Gln 493	engineered mutation
Ser 499	Gly 496	variant
Arg 501	Gln 498	variant
Tyr 504	Asn 501	variant
His 508	Tyr 505	variant
Lys 550	Thr 547	variant
Gly 617	Asp 614	variant
Tyr 658	His 655	variant
Lys 682	Asn 679	variant
His 684	Pro 681	variant
Gly 685	Arg 682	engineered mutation
Ser 686	Arg 683	engineered mutation
Ser 688	Arg 685	engineered mutation
Lys 767	Asn 764	variant
Tyr 799	Asp 796	variant
Lys 859	Asn 856	variant
His 957	Gln 954	variant
Lys 972	Asn 969	variant
Phe 984	Leu 981	variant
Pro 989	Lys 986	engineered mutation
Pro 990	Val 987	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	528241.9
Branched	Number of molecules	2
	Total formula weight	848.8
Non-Polymers*	Number of molecules	36
	Total formula weight	7963.5
All*	Total formula weight	537054.2

*Water molecules are not included.