8D56

One RBD-up state of SARS-CoV-2 BA.2 variant spike protein

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	1305	144688.2	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	a, c, D, d, f...	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	18	In PDB GlyTouCan (G62182OO)
3	b, E, F, H, O...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	9	In PDB GlyTouCan (G42666HT)
4	e, K, U	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	branched		570.5	3	In PDB GlyTouCan (G21290RB)
5	C, A, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	21	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1273 (UniProt: P0DTC2)

PDB	External Database	Details
Ile 19	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
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Ser 1274	-	expression tag
Gly 1275	-	expression tag
Gly 1276	-	expression tag
Gly 1277	-	expression tag
Ser 1278	-	expression tag
Ala 1279	-	expression tag
Trp 1280	-	expression tag
Ser 1281	-	expression tag
His 1282	-	expression tag
Pro 1283	-	expression tag
Gln 1284	-	expression tag
Phe 1285	-	expression tag
Glu 1286	-	expression tag
Lys 1287	-	expression tag
Gly 1288	-	expression tag
Gly 1289	-	expression tag
Gly 1290	-	expression tag
Ser 1291	-	expression tag
Gly 1292	-	expression tag
Gly 1293	-	expression tag
Gly 1294	-	expression tag
Ser 1295	-	expression tag
Gly 1296	-	expression tag
Gly 1297	-	expression tag
Ser 1298	-	expression tag
Ser 1299	-	expression tag
Ala 1300	-	expression tag
Trp 1301	-	expression tag
Ser 1302	-	expression tag
His 1303	-	expression tag
Pro 1304	-	expression tag
Gln 1305	-	expression tag
Phe 1306	-	expression tag
Glu 1307	-	expression tag
Lys 1308	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	3
	Total formula weight	434064.5
Branched	Number of molecules	30
	Total formula weight	16089.0
Non-Polymers*	Number of molecules	21
	Total formula weight	4645.4
All*	Total formula weight	454798.8

*Water molecules are not included.