Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with D-peptide. Determined by X-ray diffraction at 2.37 Å resolution. Released 25 Jun 2025.
Explore 9DXX in 3D Show helices and sheets RCSB PDB PDBe
9DXX contains 16 α-helices and 57 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 12-17 | 6 | 1 |
| β-strand | 18 | 1 | 2 |
| β-strand | 25-26 | 2 | 3 |
| β-strand | 34-35 | 2 | 3 |
| β-strand | 36 | 1 | 4 |
| β-strand | 39-41 | 3 | 5 |
| β-strand | 43-44 | 2 | 6 |
| β-strand | 51-54 | 4 | 7 |
| β-strand | 56 | 1 | 7 |
| α-helix | 57-58 | 2 | |
| β-strand | 59-62 | 4 | 8 |
| β-strand | 64 | 1 | 9 |
| α-helix | 66-71 | 6 | |
| α-helix | 74-79 | 6 | |
| β-strand | 83A | 1 | 10 |
| β-strand | 87-89 | 3 | 8 |
| β-strand | 95 | 1 | 9 |
| β-strand | 102 | 1 | 10 |
| α-helix | 105-112 | 8 | |
| β-strand | 115-122 | 8 | 10 |
| α-helix | 125A-126 | 4 | |
| β-strand | 131-132 | 2 | 11 |
| β-strand | 136-141 | 6 | 12 |
| β-strand | 144-146 | 3 | 12 |
| β-strand | 151-153 | 3 | 10 |
| β-strand | 154-155 | 2 | 11 |
| β-strand | 157 | 1 | 13 |
| β-strand | 160 | 1 | 13 |
| α-helix | 162-163 | 2 | |
| β-strand | 164-169 | 6 | 14 |
| β-strand | 176-184 | 9 | 10 |
| α-helix | 188-195 | 8 | |
| β-strand | 202-205 | 4 | 14 |
| β-strand | 210-213 | 4 | 14 |
| β-strand | 229-237 | 9 | 10 |
| α-helix | 238 | 1 | |
| β-strand | 242-247 | 6 | 14 |
| β-strand | 251-254 | 4 | 10 |
| β-strand | 256-262 | 7 | 10 |
| β-strand | 267-269 | 3 | 8 |
| α-helix | 272-273 | 2 | |
| β-strand | 274-279 | 6 | 7 |
| β-strand | 281-282 | 2 | 15 |
| β-strand | 287 | 1 | 15 |
| β-strand | 294-295 | 2 | 6 |
| β-strand | 301 | 1 | 16 |
| β-strand | 302-303 | 2 | 15 |
| β-strand | 305 | 1 | 17 |
| α-helix | 306 | 1 | |
| β-strand | 307-308 | 2 | 6 |
| β-strand | 315-317 | 3 | 5 |
| β-strand | 321 | 1 | 4 |
| β-strand | 324 | 1 | 18 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 6 | 1 | 19 |
| β-strand | 10 | 1 | 19 |
| β-strand | 13 | 1 | 18 |
| β-strand | 14 | 1 | 2 |
| β-strand | 22-28 | 7 | 1 |
| β-strand | 31-36 | 6 | 1 |
| α-helix | 38-59 | 22 | |
| β-strand | 62 | 1 | 17 |
| β-strand | 65 | 1 | 16 |
| α-helix | 75-126 | 52 | |
| α-helix | 127-129 | 3 | |
| β-strand | 130-134 | 5 | 1 |
| β-strand | 137-140 | 4 | 1 |
| α-helix | 146-153 | 8 | |
| α-helix | 159-170 | 12 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10 | 1 | 20 |
| α-helix | 14-16 | 3 | |
| β-strand | 23 | 1 | 21 |
| β-strand | 28 | 1 | 20 |
| β-strand | 29 | 1 | 21 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Hemagglutinin HA1 chain | A | protein | 328 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | P03452 (AlphaFold model) |
| Hemagglutinin HA2 chain | B | protein | 176 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | P03452 (AlphaFold model) |
| D-peptide | E | protein | 31 | Phage display vector pdvec0 |
>9DXX_1 Hemagglutinin HA1 chain (chains A) PGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIA GWLLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFP KESSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGI HHPPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDT IIFEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVT IGECPKYVRSAKLRMVTGLRNIPSIQSR
>9DXX_2 Hemagglutinin HA2 chain (chains B) GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMN IQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYE KVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV
>9DXX_3 D-peptide (chains E) PXRFCPSILKKCRRDSDCPGXCICKGNGYCG
| ID | Name | Formula | Copies |
|---|---|---|---|
| TOE | 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl | C7 H16 O4 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (K) are not listed.
De novo design of D-peptide ligands: Application to influenza virus hemagglutinin. Juraszek, J., Kadam, R.U., Branduardi, D. et al. Proc Natl Acad Sci U S A (2025) 122:e2426554122-e2426554122. DOI 10.1073/pnas.2426554122 · PubMed
Other PDB entries of the same protein (UniProt P03452 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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