8DZH

Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody MB.02

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 (B, A, C)	Spike glycoprotein	polymer	1285	142586.2	3	UniProt (P0DTC2) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein
2	D, F, H (E, H, I)	antibody MB.02 heavy chain	polymer	118	12972.5	3		Homo sapiens (Human)
3	E, G, I (D, L, J)	antibody MB.02 light chain	polymer	109	11683.0	3		Homo sapiens (Human)
4	AA, BA, CA, DA, EA... (a, b, c, d, e...)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	27	In PDB GlyTouCan (G42666HT)
5	AB, BB, CB, KA, LA... (C, B, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	19	Chemie (NAG)

Sequence modifications

B, A, C: 1 - 1205 (UniProt: P0DTC2)

PDB	External Database	Details
Val 67	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
Ile 93	Thr 95	variant
-	Gly 142	deletion
-	Val 143	deletion
-	Tyr 144	deletion
Asp 140	Tyr 145	conflict
Ile 206	-	insertion
Val 207	-	insertion
Arg 208	Asn 211	conflict
Glu 209	Leu 212	conflict
Pro 210	Val 213	conflict
Glu 211	Arg 214	conflict
Asp 336	Gly 339	conflict
Leu 368	Ser 371	conflict
Pro 370	Ser 373	conflict
Phe 372	Ser 375	conflict
Asn 414	Lys 417	variant
Lys 437	Asn 440	conflict
Ser 443	Gly 446	conflict
Asn 474	Ser 477	variant
Lys 475	Thr 478	variant
Ala 481	Glu 484	conflict
Arg 490	Gln 493	conflict
Ser 493	Gly 496	conflict
Arg 495	Gln 498	conflict
Tyr 498	Asn 501	variant
His 502	Tyr 505	conflict
Lys 544	Thr 547	conflict
Gly 611	Asp 614	variant
Tyr 652	His 655	variant
Lys 676	Asn 679	conflict
His 678	Pro 681	variant
Gly 679	Arg 682	conflict
Ser 680	Arg 683	conflict
Ser 682	Arg 685	conflict
Lys 761	Asn 764	conflict
Tyr 793	Asp 796	variant
Pro 814	Phe 817	conflict
Lys 853	Asn 856	conflict
Pro 889	Ala 892	conflict
Pro 896	Ala 899	conflict
Pro 939	Ala 942	conflict
His 951	Gln 954	conflict
Lys 966	Asn 969	conflict
Phe 978	Leu 981	conflict
Pro 983	Lys 986	conflict
Pro 984	Val 987	conflict
Gly 1206	-	expression tag
Ser 1207	-	expression tag
Gly 1208	-	expression tag
Tyr 1209	-	expression tag
Ile 1210	-	expression tag
Pro 1211	-	expression tag
Glu 1212	-	expression tag
Ala 1213	-	expression tag
Pro 1214	-	expression tag
Arg 1215	-	expression tag
Asp 1216	-	expression tag
Gly 1217	-	expression tag
Gln 1218	-	expression tag
Ala 1219	-	expression tag
Tyr 1220	-	expression tag
Val 1221	-	expression tag
Arg 1222	-	expression tag
Lys 1223	-	expression tag
Asp 1224	-	expression tag
Gly 1225	-	expression tag
Glu 1226	-	expression tag
Trp 1227	-	expression tag
Val 1228	-	expression tag
Leu 1229	-	expression tag
Leu 1230	-	expression tag
Ser 1231	-	expression tag
Thr 1232	-	expression tag
Phe 1233	-	expression tag
Leu 1234	-	expression tag
Gly 1235	-	expression tag
Arg 1236	-	expression tag
Ser 1237	-	expression tag
Leu 1238	-	expression tag
Glu 1239	-	expression tag
Val 1240	-	expression tag
Leu 1241	-	expression tag
Phe 1242	-	expression tag
Gln 1243	-	expression tag
Gly 1244	-	expression tag
Pro 1245	-	expression tag
Gly 1246	-	expression tag
His 1247	-	expression tag
His 1248	-	expression tag
His 1249	-	expression tag
His 1250	-	expression tag
His 1251	-	expression tag
His 1252	-	expression tag
His 1253	-	expression tag
His 1254	-	expression tag
Ser 1255	-	expression tag
Ala 1256	-	expression tag
Trp 1257	-	expression tag
Ser 1258	-	expression tag
His 1259	-	expression tag
Pro 1260	-	expression tag
Gln 1261	-	expression tag
Phe 1262	-	expression tag
Glu 1263	-	expression tag
Lys 1264	-	expression tag
Gly 1265	-	expression tag
Gly 1266	-	expression tag
Gly 1267	-	expression tag
Ser 1268	-	expression tag
Gly 1269	-	expression tag
Gly 1270	-	expression tag
Gly 1271	-	expression tag
Gly 1272	-	expression tag
Ser 1273	-	expression tag
Gly 1274	-	expression tag
Gly 1275	-	expression tag
Ser 1276	-	expression tag
Ala 1277	-	expression tag
Trp 1278	-	expression tag
Ser 1279	-	expression tag
His 1280	-	expression tag
Pro 1281	-	expression tag
Gln 1282	-	expression tag
Phe 1283	-	expression tag
Glu 1284	-	expression tag
Lys 1285	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	501724.9
Branched	Number of molecules	27
	Total formula weight	11458.8
Non-Polymers*	Number of molecules	19
	Total formula weight	4203.0
All*	Total formula weight	517386.7

*Water molecules are not included.