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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9D8H

JN.1 SARS-COV-2 Spike 3-down conformation

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, B, C
(A, B, C)		Spike glycoproteinpolymer1305144602.13UniProt (P0DTC2)
Pfam (PF16451)
Pfam (PF09408)
Pfam (PF19209)
Pfam (PF01601)		Severe acute respiratory syndrome coronavirus 2S glycoprotein,E2,Peplomer protein
2D, E, F, H, I...
(D, E, F, H, I...)		2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched424.412In PDB
GlyTouCan (G42666HT)
3G, L, Q
(G, L, Q)		2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranosebranched570.53In PDB
GlyTouCan (G21290RB)
4AA, BA, CA, DA, EA...
(A, B, C)		2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.230Chemie (NAG)
Sequence modifications
A, B, C: 29 - 1269 (UniProt: P0DTC2)
PDBExternal DatabaseDetails
Met 1-initiating methionine
Phe 2-expression tag
Val 3-expression tag
Phe 4-expression tag
Leu 5-expression tag
Val 6-expression tag
Leu 7-expression tag
Leu 8-expression tag
Pro 9-expression tag
Leu 10-expression tag
Val 11-expression tag
Ser 12-expression tag
Ser 13-expression tag
Gln 14-expression tag
Cys 15-expression tag
Val 16-expression tag
Met 17-expression tag
Pro 18-expression tag
Leu 19-expression tag
Phe 20-expression tag
Asn 21-expression tag
Leu 22-expression tag
Ile 23-expression tag
Thr 24-expression tag
Thr 25-expression tag
Thr 26-expression tag
Gln 27-expression tag
Ser 28-expression tag
Leu 51Ser 50conflict
-His 69deletion
-Val 70deletion
Phe 126Val 127conflict
Asp 141Gly 142conflict
-Tyr 144deletion
Ser 155Phe 157conflict
Gly 156Arg 158conflict
-Asn 211deletion
Ile 209Leu 212conflict
Gly 210Val 213conflict
Phe 213Leu 216conflict
Asn 242His 245conflict
Asp 261Ala 264conflict
Val 329Ile 332conflict
His 336Gly 339conflict
Thr 353Lys 356conflict
Phe 368Ser 371conflict
Pro 370Ser 373conflict
Phe 372Ser 375conflict
Ala 373Thr 376conflict
Lys 400Arg 403conflict
Asn 402Asp 405conflict
Ser 405Arg 408conflict
Asn 414Lys 417conflict
Lys 437Asn 440conflict
His 442Val 445conflict
Ser 443Gly 446conflict
Asp 447Asn 450conflict
Trp 449Leu 452conflict
Ser 452Leu 455conflict
Lys 457Asn 460conflict
Asn 474Ser 477conflict
Lys 475Thr 478conflict
Lys 478Asn 481conflict
-Val 483deletion
Lys 480Glu 484conflict
Pro 482Phe 486conflict
Arg 494Gln 498conflict
Tyr 497Asn 501conflict
His 501Tyr 505conflict
Lys 550Glu 554conflict
Val 566Ala 570conflict
Gly 610Asp 614conflict
Ser 617Pro 621conflict
Tyr 651His 655conflict
Lys 675Asn 679conflict
Arg 677Pro 681conflict
Lys 760Asn 764conflict
Tyr 792Asp 796conflict
Phe 935Ser 939conflict
His 950Gln 954conflict
Lys 965Asn 969conflict
Pro 982Lys 986conflict
Pro 983Val 987conflict
Leu 1139Pro 1143conflict
Gly 1270-expression tag
Gly 1271-expression tag
Gly 1272-expression tag
Gly 1273-expression tag
Ser 1274-expression tag
Gly 1275-expression tag
Gly 1276-expression tag
Gly 1277-expression tag
Gly 1278-expression tag
Ser 1279-expression tag
Trp 1280-expression tag
Ser 1281-expression tag
His 1282-expression tag
Pro 1283-expression tag
Gln 1284-expression tag
Phe 1285-expression tag
Glu 1286-expression tag
Lys 1287-expression tag
Gly 1288-expression tag
Gly 1289-expression tag
Gly 1290-expression tag
Gly 1291-expression tag
Ser 1292-expression tag
Gly 1293-expression tag
Gly 1294-expression tag
Gly 1295-expression tag
Gly 1296-expression tag
Ser 1297-expression tag
Trp 1298-expression tag
Ser 1299-expression tag
His 1300-expression tag
Pro 1301-expression tag
Gln 1302-expression tag
Phe 1303-expression tag
Glu 1304-expression tag
Lys 1305-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains3
Total formula weight433806.2
BranchedNumber of molecules15
Total formula weight6804.4
Non-Polymers*Number of molecules30
Total formula weight6636.2
All*Total formula weight447246.9
*Water molecules are not included.

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PDB entries from 2025-11-05

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