Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with small molecule JNJ4796. Determined by X-ray diffraction at 2.32 Å resolution. Released 13 Feb 2019.
Explore 6CFG in 3D Show helices and sheets RCSB PDB PDBe
6CFG contains 17 α-helices and 48 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 |
|---|---|---|---|
| α-helix | 9-11 | 3 | |
| 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 | 59-60 | 2 | 8 |
| β-strand | 64 | 1 | 9 |
| α-helix | 66-71 | 6 | |
| α-helix | 74-79 | 6 | |
| α-helix | 82-83A | 3 | |
| β-strand | 87-89 | 3 | 8 |
| β-strand | 95 | 1 | 9 |
| β-strand | 100-102 | 3 | 10 |
| α-helix | 105-112 | 8 | |
| β-strand | 115-122 | 8 | 10 |
| α-helix | 125A-126 | 3 | |
| 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 |
| 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 | 223 | 1 | 15 |
| β-strand | 226 | 1 | 15 |
| 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 | 8 | 10 |
| β-strand | 267-269 | 3 | 8 |
| β-strand | 274-279 | 6 | 7 |
| β-strand | 281-283 | 3 | 16 |
| β-strand | 286-287 | 2 | 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 |
| α-helix | 322-323 | 2 |
| 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 | 38-58 | 21 | |
| α-helix | 75-126 | 52 | |
| α-helix | 127-129 | 3 | |
| β-strand | 130-132 | 3 | 1 |
| β-strand | 137-140 | 4 | 1 |
| α-helix | 146-153 | 8 | |
| α-helix | 159-175 | 17 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Hemagglutinin | A | protein | 334 | Influenza A virus (A/Viet Nam/1203/2004(H5N1)) | Q5EP31 |
| Hemagglutinin | B | protein | 177 | Influenza A virus (A/Viet Nam/1203/2004(H5N1)) | Q6DQ18 |
>6CFG_1 Hemagglutinin (chains A) ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLW GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPN DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP LTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR
>6CFG_2 Hemagglutinin (chains B) GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| EZ7 | N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl… | C28 H27 N9 O3 | 1 |
Water and common crystallization additives (PEG) are not listed.
A small-molecule fusion inhibitor of influenza virus is orally active in mice. van Dongen, M.J.P., Kadam, R.U., Juraszek, J. et al. Science (2019) 363. DOI 10.1126/science.aar6221 · PubMed
Other PDB entries of the same protein (UniProt Q5EP31), best resolution first:
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