8R1D

SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein

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 (F, D, H)	SD1-3 Fab Heavy Chain	polymer	121	12914.3	3		Homo sapiens
2	D, H, I (L, E, G)	SD1-3 Fab Light Chain	polymer	106	11218.3	3		Homo sapiens
3	E, F, G (A, B, C)	Spike glycoprotein,Fibritin	polymer	1285	142729.3	3	UniProt (P0DTC2) UniProt (P10104) Pfam (PF16451) Pfam (PF09408) Pfam (PF19209) Pfam (PF01601)	Homo sapiens (human)	S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein
4	AA, BA, CA, DA, EA... (B, C, A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	30	Chemie (NAG)
5	NA, OA, PA, QA, RA... (F, H, A, B, C...)	water	water		18.0	43	Chemie (HOH)

Sequence modifications

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

PDB	External Database	Details
Ile 19	Thr 19	variant
Ser 24	Leu 24	variant
-	Pro 25	deletion
-	Pro 26	deletion
-	Ala 27	deletion
Asp 139	Gly 142	variant
Gly 210	Val 213	variant
Asp 336	Gly 339	variant
Phe 368	Ser 371	variant
Pro 370	Ser 373	variant
Phe 372	Ser 375	variant
Ala 373	Thr 376	variant
Asn 402	Asp 405	variant
Ser 405	Arg 408	variant
Asn 414	Lys 417	variant
Lys 437	Asn 440	variant
Gln 449	Leu 452	variant
Asn 474	Ser 477	variant
Lys 475	Thr 478	variant
Ala 481	Glu 484	engineered mutation
Arg 490	Gln 493	variant
Arg 495	Gln 498	variant
Tyr 498	Asn 501	variant
His 502	Tyr 505	variant
Gly 611	Asp 614	variant
Tyr 652	His 655	variant
Lys 676	Asn 679	variant
His 678	Pro 681	variant
Leu 701	Ser 704	variant
Lys 761	Asn 764	variant
Tyr 793	Asp 796	variant
His 951	Gln 954	variant
Lys 966	Asn 969	variant
Gly 1206	-	linker
Ser 1207	-	linker

A, B, C: 1208 - 1234 (UniProt: P10104)

PDB	External Database	Details
Leu 1229	Phe 479	engineered mutation
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
Gly 1255	-	expression tag
Ser 1256	-	expression tag
Ala 1257	-	expression tag
Trp 1258	-	expression tag
Ser 1259	-	expression tag
His 1260	-	expression tag
Pro 1261	-	expression tag
Gln 1262	-	expression tag
Phe 1263	-	expression tag
Glu 1264	-	expression tag
Lys 1265	-	expression tag
Gly 1266	-	expression tag
Gly 1267	-	expression tag
Gly 1268	-	expression tag
Ser 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	500585.5
Non-Polymers*	Number of molecules	30
	Total formula weight	6636.2
All*	Total formula weight	507221.8

*Water molecules are not included.