Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141076 (CP8). Determined by X-ray diffraction at 1.59 Å resolution. Released 24 Dec 2025.
Explore 9PHD in 3D Show helices and sheets RCSB PDB PDBe
9PHD contains 11 α-helices and 49 β-strands across 2 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 | 50-54 | 5 | 7 |
| β-strand | 56 | 1 | 7 |
| 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 |
| β-strand | 131 | 1 | 11 |
| β-strand | 136-141 | 6 | 12 |
| β-strand | 144-146 | 3 | 12 |
| β-strand | 151-153 | 3 | 10 |
| β-strand | 155 | 1 | 11 |
| β-strand | 157 | 1 | 13 |
| β-strand | 160 | 1 | 13 |
| 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 | 223 | 1 | 15 |
| β-strand | 226 | 1 | 15 |
| β-strand | 229-237 | 9 | 10 |
| 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 | 1 | |
| β-strand | 273-279 | 7 | 7 |
| β-strand | 281-283 | 3 | 16 |
| β-strand | 286-288 | 3 | 16 |
| β-strand | 294-295 | 2 | 6 |
| β-strand | 302-303 | 2 | 16 |
| α-helix | 306 | 1 | |
| β-strand | 307-308 | 2 | 6 |
| β-strand | 315-317 | 3 | 5 |
| β-strand | 321 | 1 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 6 | 1 | 17 |
| β-strand | 10 | 1 | 17 |
| β-strand | 14 | 1 | 2 |
| β-strand | 22-28 | 7 | 1 |
| β-strand | 31-36 | 6 | 1 |
| α-helix | 38-55 | 18 | |
| α-helix | 75-126 | 52 | |
| α-helix | 127-129 | 3 | |
| β-strand | 130-132 | 3 | 1 |
| β-strand | 137-140 | 4 | 1 |
| α-helix | 146-154 | 9 | |
| α-helix | 159-170 | 12 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Hemagglutinin | C | protein | 326 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | P03452 (AlphaFold model) |
| Hemagglutinin HA2 chain | D | protein | 176 | Influenza A virus (A/Puerto Rico/8/1934(H1N1)) | P03452 (AlphaFold model) |
| cyclic peptide CP141076 | G | protein | 15 | synthetic construct |
>9PHD_1 Hemagglutinin (chains C) DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAGW LLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPKE SSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIHH PPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTII FEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIG ECPKYVRSAKLRMVTGLRNIPSIQSR
>9PHD_2 Hemagglutinin HA2 chain (chains D) GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMN IQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYE KVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV
>9PHD_3 cyclic peptide CP141076 (chains G) CLYRDPLGVAGGMGC
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Water and common crystallization additives (GOL, PEG, SO4) are not listed.
V H H antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion. Kadam, R.U., Juraszek, J., Brandenburg, B. et al. Npj Viruses (2025) 3:83-83. DOI 10.1038/s44298-025-00166-1 · 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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