8VYF

SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Spike glycoprotein	polymer	1270	140929.2	1	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	B	S2L20 Heavy Chain	polymer	122	13541.0	1		Homo sapiens
3	C	S2L20 Light Chain	polymer	107	11829.1	1		Homo sapiens
4	H	S2X303 Heavy Chain	polymer	125	13737.7	1		Homo sapiens
5	L	S2X303 Light Chain	polymer	105	11270.3	1		Homo sapiens
6	D	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		586.5	1	In PDB GlyTouCan (G15407YE)
7	E, F	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
8	A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	5	Chemie (NAG)

Sequence modifications

A: 1 - 1201 (UniProt: P0DTC2)

PDB	External Database	Details
Val 75	Gly 75	variant
Ile 76	Thr 76	variant
-	Arg 246	deletion
-	Ser 247	deletion
-	Tyr 248	deletion
-	Leu 249	deletion
-	Thr 250	deletion
-	Pro 251	deletion
-	Gly 252	deletion
Asn 246	Asp 253	variant
Cys 376	Ser 383	conflict
Gln 445	Leu 452	variant
Ser 483	Phe 490	variant
Gly 607	Asp 614	variant
Pro 810	Phe 817	conflict
Asn 852	Thr 859	variant
Pro 885	Ala 892	conflict
Pro 892	Ala 899	conflict
Pro 935	Ala 942	conflict
Cys 978	Asp 985	conflict
Pro 979	Lys 986	conflict
Pro 980	Val 987	conflict
Gly 1202	-	expression tag
Ser 1203	-	expression tag
Gly 1204	-	expression tag
Tyr 1205	-	expression tag
Ile 1206	-	expression tag
Pro 1207	-	expression tag
Glu 1208	-	expression tag
Ala 1209	-	expression tag
Pro 1210	-	expression tag
Arg 1211	-	expression tag
Asp 1212	-	expression tag
Gly 1213	-	expression tag
Gln 1214	-	expression tag
Ala 1215	-	expression tag
Tyr 1216	-	expression tag
Val 1217	-	expression tag
Arg 1218	-	expression tag
Lys 1219	-	expression tag
Asp 1220	-	expression tag
Gly 1221	-	expression tag
Glu 1222	-	expression tag
Trp 1223	-	expression tag
Val 1224	-	expression tag
Leu 1225	-	expression tag
Leu 1226	-	expression tag
Ser 1227	-	expression tag
Thr 1228	-	expression tag
Phe 1229	-	expression tag
Leu 1230	-	expression tag
Gly 1231	-	expression tag
Arg 1232	-	expression tag
Ser 1233	-	expression tag
Leu 1234	-	expression tag
Glu 1235	-	expression tag
Val 1236	-	expression tag
Leu 1237	-	expression tag
Phe 1238	-	expression tag
Gln 1239	-	expression tag
Gly 1240	-	expression tag
Pro 1241	-	expression tag
Gly 1242	-	expression tag
Ser 1243	-	expression tag
Gly 1244	-	expression tag
Gly 1245	-	expression tag
Leu 1246	-	expression tag
Asn 1247	-	expression tag
Asp 1248	-	expression tag
Ile 1249	-	expression tag
Phe 1250	-	expression tag
Glu 1251	-	expression tag
Ala 1252	-	expression tag
Gln 1253	-	expression tag
Lys 1254	-	expression tag
Ile 1255	-	expression tag
Glu 1256	-	expression tag
Trp 1257	-	expression tag
His 1258	-	expression tag
Glu 1259	-	expression tag
Gly 1260	-	expression tag
Ser 1261	-	expression tag
Gly 1262	-	expression tag
His 1263	-	expression tag
His 1264	-	expression tag
His 1265	-	expression tag
His 1266	-	expression tag
His 1267	-	expression tag
His 1268	-	expression tag
His 1269	-	expression tag
His 1270	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	5
	Total formula weight	191307.4
Branched	Number of molecules	3
	Total formula weight	1435.3
Non-Polymers*	Number of molecules	5
	Total formula weight	1106.0
All*	Total formula weight	193848.7

*Water molecules are not included.