8ERR

SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment

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	1274	141870.7	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	H, E, I	S2X324 heavy chain	polymer	119	13201.0	3		Homo sapiens
3	L, F, J	S2X324 light chain	polymer	110	11513.6	3		Homo sapiens
4	D	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	1	In PDB GlyTouCan (G42666HT)
5	B, C, A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	48	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 210 (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

A, B, C: 210 - 1207 (UniProt: P0DTC2)

PDB	External Database	Details
Ile 210	Leu 212	variant
Glu 210	-	insertion
Pro 210	-	insertion
Glu 210	-	insertion
Asp 339	Gly 339	variant
Leu 371	Ser 371	variant
Pro 373	Ser 373	variant
Phe 375	Ser 375	variant
Asn 417	Lys 417	variant
Lys 440	Asn 440	variant
Ser 446	Gly 446	variant
Asn 477	Ser 477	variant
Lys 478	Thr 478	variant
Ala 484	Glu 484	variant
Arg 493	Gln 493	variant
Ser 496	Gly 496	variant
Arg 498	Gln 498	variant
Tyr 501	Asn 501	variant
His 505	Tyr 505	variant
Lys 547	Thr 547	variant
Gly 614	Asp 614	variant
Tyr 655	His 655	variant
Lys 679	Asn 679	variant
His 681	Pro 681	variant
Cys 707	Tyr 707	variant
Lys 764	Asn 764	variant
Tyr 796	Asp 796	variant
Pro 817	Phe 817	variant
Lys 856	Asn 856	variant
Cys 883	Thr 883	variant
Pro 892	Ala 892	variant
Pro 899	Ala 899	variant
Pro 942	Ala 942	variant
His 954	Gln 954	variant
Lys 969	Asn 969	variant
Phe 981	Leu 981	variant
Pro 987	Val 987	variant
Gln 1208	-	expression tag
Gly 1209	-	expression tag
Ser 1210	-	expression tag
Gly 1211	-	expression tag
Tyr 1212	-	expression tag
Ile 1213	-	expression tag
Pro 1214	-	expression tag
Glu 1215	-	expression tag
Ala 1216	-	expression tag
Pro 1217	-	expression tag
Arg 1218	-	expression tag
Asp 1219	-	expression tag
Gly 1220	-	expression tag
Gln 1221	-	expression tag
Ala 1222	-	expression tag
Tyr 1223	-	expression tag
Val 1224	-	expression tag
Arg 1225	-	expression tag
Lys 1226	-	expression tag
Asp 1227	-	expression tag
Gly 1228	-	expression tag
Glu 1229	-	expression tag
Trp 1230	-	expression tag
Val 1231	-	expression tag
Leu 1232	-	expression tag
Leu 1233	-	expression tag
Ser 1234	-	expression tag
Thr 1235	-	expression tag
Phe 1236	-	expression tag
Leu 1237	-	expression tag
Gly 1238	-	expression tag
Arg 1239	-	expression tag
Ser 1240	-	expression tag
Leu 1241	-	expression tag
Glu 1242	-	expression tag
Val 1243	-	expression tag
Leu 1244	-	expression tag
Phe 1245	-	expression tag
Gln 1246	-	expression tag
Gly 1247	-	expression tag
Pro 1248	-	expression tag
Gly 1249	-	expression tag
Ser 1250	-	expression tag
Gly 1251	-	expression tag
Gly 1252	-	expression tag
Leu 1253	-	expression tag
Asn 1254	-	expression tag
Asp 1255	-	expression tag
Ile 1256	-	expression tag
Phe 1257	-	expression tag
Glu 1258	-	expression tag
Ala 1259	-	expression tag
Gln 1260	-	expression tag
Lys 1261	-	expression tag
Ile 1262	-	expression tag
Glu 1263	-	expression tag
Trp 1264	-	expression tag
His 1265	-	expression tag
Glu 1266	-	expression tag
Gly 1267	-	expression tag
Ser 1268	-	expression tag
Gly 1269	-	expression tag
His 1270	-	expression tag
His 1271	-	expression tag
His 1272	-	expression tag
His 1273	-	expression tag
His 1274	-	expression tag
His 1275	-	expression tag
His 1276	-	expression tag
His 1277	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	499756.0
Branched	Number of molecules	1
	Total formula weight	424.4
Non-Polymers*	Number of molecules	48
	Total formula weight	10618.0
All*	Total formula weight	510798.4

*Water molecules are not included.