8XKI

A neutralizing nanobody VHH60 against wt SARS-CoV-2

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	D	nanobody VHH60	polymer	121	13410.9	1		synthetic construct
2	A, B, C	Spike glycoprotein	polymer	1288	142347.3	3	UniProt (P0DTC2) In PDB	Severe acute respiratory syndrome coronavirus 2 (2019-nCoV SARS-CoV-2)	S glycoprotein,E2,Peplomer protein
3	K, O, P, Q, T...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	6	In PDB GlyTouCan (G42666HT)
4	C, A, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	20	Chemie (NAG)

Sequence modifications

A, B, C: 1 - 1208 (UniProt: P0DTC2)

PDB	External Database	Details
Gly 682	Arg 682	variant
Ser 683	Arg 683	variant
Ser 685	Arg 685	variant
Pro 817	Phe 817	variant
Pro 892	Ala 892	variant
Pro 899	Ala 899	variant
Pro 942	Ala 942	variant
Pro 986	Lys 986	variant
Pro 987	Val 987	variant
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
Phe 1232	-	expression tag
Leu 1233	-	expression tag
Ser 1234	-	expression tag
Thr 1235	-	expression tag
Phe 1236	-	expression tag
Leu 1237	-	expression tag
Ser 1238	-	expression tag
Gly 1239	-	expression tag
Leu 1240	-	expression tag
Glu 1241	-	expression tag
Val 1242	-	expression tag
Leu 1243	-	expression tag
Phe 1244	-	expression tag
Gln 1245	-	expression tag
Gly 1246	-	expression tag
Pro 1247	-	expression tag
Gly 1248	-	expression tag
Gly 1249	-	expression tag
Trp 1250	-	expression tag
Ser 1251	-	expression tag
His 1252	-	expression tag
Pro 1253	-	expression tag
Gln 1254	-	expression tag
Phe 1255	-	expression tag
Glu 1256	-	expression tag
Lys 1257	-	expression tag
Gly 1258	-	expression tag
Gly 1259	-	expression tag
Gly 1260	-	expression tag
Ser 1261	-	expression tag
Gly 1262	-	expression tag
Gly 1263	-	expression tag
Gly 1264	-	expression tag
Ser 1265	-	expression tag
Gly 1266	-	expression tag
Gly 1267	-	expression tag
Ser 1268	-	expression tag
Ala 1269	-	expression tag
Trp 1270	-	expression tag
Ser 1271	-	expression tag
His 1272	-	expression tag
Pro 1273	-	expression tag
Gln 1274	-	expression tag
Phe 1275	-	expression tag
Glu 1276	-	expression tag
Lys 1277	-	expression tag
Gly 1278	-	expression tag
Gly 1279	-	expression tag
Ser 1280	-	expression tag
His 1281	-	expression tag
His 1282	-	expression tag
His 1283	-	expression tag
His 1284	-	expression tag
His 1285	-	expression tag
His 1286	-	expression tag
His 1287	-	expression tag
His 1288	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	440452.7
Branched	Number of molecules	6
	Total formula weight	2546.4
Non-Polymers*	Number of molecules	20
	Total formula weight	4424.2
All*	Total formula weight	447423.3

*Water molecules are not included.