9FGU

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	C	Spike glycoprotein,Fibritin	polymer	1214	135255.2	1	UniProt (P0DTC2) UniProt (P10104) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601) In PDB	Severe acute respiratory syndrome coronavirus 2	S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein
2	E	scFv76-77 single chain fragment	polymer	265	28197.2	1		Homo sapiens
3	C	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	1	Chemie (NAG)

Sequence modifications

C: 16 - 1149 (UniProt: P0DTC2)

PDB	External Database	Details
Val 82	Ala 67	variant
-	His 69	deletion
-	Val 70	deletion
-	Ser 71	deletion
-	Gly 72	deletion
-	Thr 73	deletion
-	Asn 74	deletion
-	Gly 75	deletion
-	Thr 76	deletion
Ser 84	Lys 77	conflict
Ile 102	Thr 95	variant
Asp 149	Gly 142	variant
Ile 218	Asn 211	variant
Val 219	Leu 212	variant
Pro 220	Val 213	variant
Glu 221	Arg 214	variant
-	Ser 247	deletion
-	Tyr 248	deletion
-	Leu 249	deletion
-	Thr 250	deletion
-	Pro 251	deletion
-	Gly 252	deletion
-	Asp 253	deletion
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	conflict
Lys 547	Thr 547	conflict
Gly 614	Asp 614	conflict
-	Pro 621	deletion
-	Val 622	deletion
-	Ala 623	deletion
-	Ile 624	deletion
-	His 625	deletion
-	Ala 626	deletion
-	Asp 627	deletion
-	Gln 628	deletion
-	Leu 629	deletion
-	Thr 630	deletion
-	Pro 631	deletion
-	Thr 632	deletion
-	Trp 633	deletion
-	Arg 634	deletion
-	Val 635	deletion
-	Tyr 636	deletion
-	Ser 637	deletion
-	Thr 638	deletion
-	Gly 639	deletion
-	Ser 640	deletion
Tyr 635	His 655	conflict
-	Gln 677	deletion
-	Thr 678	deletion
-	Asn 679	deletion
-	Ser 680	deletion
-	Pro 681	deletion
-	Arg 682	deletion
-	Arg 683	deletion
-	Ala 684	deletion
-	Arg 685	deletion
-	Ser 686	deletion
-	Val 687	deletion
-	Ala 688	deletion
Lys 732	Asn 764	conflict
Tyr 764	Asp 796	conflict
-	Pro 812	deletion
-	Leu 828	deletion
-	Ala 829	deletion
-	Asp 830	deletion
-	Ala 831	deletion
-	Gly 832	deletion
-	Phe 833	deletion
-	Ile 834	deletion
-	Lys 835	deletion
-	Gln 836	deletion
-	Tyr 837	deletion
-	Gly 838	deletion
-	Asp 839	deletion
-	Cys 840	deletion
-	Leu 841	deletion
-	Gly 842	deletion
-	Asp 843	deletion
-	Ile 844	deletion
-	Ala 845	deletion
-	Ala 846	deletion
-	Arg 847	deletion
-	Asp 848	deletion
-	Leu 849	deletion
-	Ile 850	deletion
-	Cys 851	deletion
-	Ala 852	deletion
-	Gln 853	deletion
Lys 797	Asn 856	conflict
His 895	Gln 954	conflict
Lys 910	Asn 969	conflict
Phe 922	Leu 981	conflict
Pro 927	Lys 986	conflict
Pro 928	Val 987	conflict
Gly 1150	-	linker
Ser 1151	-	linker

C: 1152 - 1178 (UniProt: P10104)

PDB	External Database	Details
Leu 1173	Phe 479	conflict
Gly 1179	-	expression tag
Arg 1180	-	expression tag
Ser 1181	-	expression tag
Leu 1182	-	expression tag
Glu 1183	-	expression tag
Val 1184	-	expression tag
Leu 1185	-	expression tag
Phe 1186	-	expression tag
Gln 1187	-	expression tag
Gly 1188	-	expression tag
Pro 1189	-	expression tag
Gly 1190	-	expression tag
His 1191	-	expression tag
His 1192	-	expression tag
His 1193	-	expression tag
His 1194	-	expression tag
His 1195	-	expression tag
His 1196	-	expression tag
His 1197	-	expression tag
His 1198	-	expression tag
Ser 1199	-	expression tag
Ala 1200	-	expression tag
Trp 1201	-	expression tag
Ser 1202	-	expression tag
His 1203	-	expression tag
Pro 1204	-	expression tag
Gln 1205	-	expression tag
Phe 1206	-	expression tag
Glu 1207	-	expression tag
Lys 1208	-	expression tag
Gly 1209	-	expression tag
Gly 1210	-	expression tag
Gly 1211	-	expression tag
Ser 1212	-	expression tag
Gly 1213	-	expression tag
Gly 1214	-	expression tag
Gly 1215	-	expression tag
Gly 1216	-	expression tag
Ser 1217	-	expression tag
Gly 1218	-	expression tag
Gly 1219	-	expression tag
Ser 1220	-	expression tag
Ala 1221	-	expression tag
Trp 1222	-	expression tag
Ser 1223	-	expression tag
His 1224	-	expression tag
Pro 1225	-	expression tag
Gln 1226	-	expression tag
Phe 1227	-	expression tag
Glu 1228	-	expression tag
Lys 1229	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	163452.3
Non-Polymers*	Number of molecules	1
	Total formula weight	221.2
All*	Total formula weight	163673.5

*Water molecules are not included.