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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8DM2

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein (focused refinement of NTD)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(A)		Spike glycoproteinpolymer1285142441.81UniProt (P0DTC2)
Pfam (PF16451)
Pfam (PF09408)
Pfam (PF19209)
Pfam (PF01601)		Severe acute respiratory syndrome coronavirus 2S glycoprotein,E2,Peplomer protein
2B
(B)		2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched424.41In PDB
GlyTouCan (G42666HT)
3C, D, E, F
(A)		2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.24Chemie (NAG)
Sequence modifications
A: 1 - 1208 (UniProt: P0DTC2)
PDBExternal DatabaseDetails
Ile 19Thr 19conflict
-Leu 24deletion
-Pro 25deletion
-Pro 26deletion
Ser 27Ala 27conflict
Asp 142Gly 142conflict
Gly 213Val 213conflict
Asp 339Gly 339conflict
Phe 371Ser 371conflict
Pro 373Ser 373conflict
Phe 375Ser 375conflict
Ala 376Thr 376conflict
Asn 405Asp 405conflict
Ser 408Arg 408conflict
Asn 417Lys 417conflict
Lys 440Asn 440conflict
Asn 477Ser 477conflict
Lys 478Thr 478conflict
Ala 484Glu 484conflict
Arg 493Gln 493conflict
Arg 498Gln 498conflict
Tyr 501Asn 501conflict
His 505Tyr 505conflict
Gly 614Asp 614conflict
Tyr 655His 655conflict
Lys 679Asn 679conflict
His 681Pro 681conflict
Gly 682Arg 682conflict
Ser 683Arg 683conflict
Ser 685Arg 685conflict
Lys 764Asn 764conflict
Tyr 796Asp 796conflict
Pro 817Phe 817conflict
Pro 892Ala 892conflict
Pro 899Ala 899conflict
Pro 942Ala 942conflict
His 954Gln 954conflict
Lys 969Asn 969conflict
Pro 986Lys 986conflict
Pro 987Val 987conflict
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
Leu 1232-expression tag
Leu 1233-expression tag
Ser 1234-expression tag
Thr 1235-expression tag
Phe 1236-expression tag
Leu 1237-expression tag
Gly 1238-expression tag
Arg 1239-expression tag
Ser 1240-expression tag
Leu 1241-expression tag
Glu 1242-expression tag
Val 1243-expression tag
Leu 1244-expression tag
Phe 1245-expression tag
Gln 1246-expression tag
Gly 1247-expression tag
Pro 1248-expression tag
Gly 1249-expression tag
His 1250-expression tag
His 1251-expression tag
His 1252-expression tag
His 1253-expression tag
His 1254-expression tag
His 1255-expression tag
His 1256-expression tag
His 1257-expression tag
Ser 1258-expression tag
Ala 1259-expression tag
Trp 1260-expression tag
Ser 1261-expression tag
His 1262-expression tag
Pro 1263-expression tag
Gln 1264-expression tag
Phe 1265-expression tag
Glu 1266-expression tag
Lys 1267-expression tag
Gly 1268-expression tag
Gly 1269-expression tag
Gly 1270-expression tag
Ser 1271-expression tag
Gly 1272-expression tag
Gly 1273-expression tag
Gly 1274-expression tag
Gly 1275-expression tag
Ser 1276-expression tag
Gly 1277-expression tag
Gly 1278-expression tag
Ser 1279-expression tag
Ala 1280-expression tag
Trp 1281-expression tag
Ser 1282-expression tag
His 1283-expression tag
Pro 1284-expression tag
Gln 1285-expression tag
Phe 1286-expression tag
Glu 1287-expression tag
Lys 1288-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains1
Total formula weight142441.8
BranchedNumber of molecules1
Total formula weight424.4
Non-Polymers*Number of molecules4
Total formula weight884.8
All*Total formula weight143751.0
*Water molecules are not included.

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PDB entries from 2025-05-21

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