Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PuertoRico/8/1934). Determined by X-ray diffraction at 1.8 Å resolution. Released 27 Sept 2017.
Explore 5VLI in 3D Show helices and sheets RCSB PDB PDBe
5VLI contains 13 α-helices and 53 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 | 7-12 | 6 | 1 |
| β-strand | 13 | 1 | 2 |
| β-strand | 20-21 | 2 | 3 |
| β-strand | 29-30 | 2 | 3 |
| β-strand | 31 | 1 | 4 |
| β-strand | 34-36 | 3 | 5 |
| β-strand | 38-39 | 2 | 6 |
| β-strand | 45-49 | 5 | 7 |
| β-strand | 51 | 1 | 7 |
| β-strand | 54-57 | 4 | 8 |
| β-strand | 59 | 1 | 9 |
| α-helix | 61-66 | 6 | |
| α-helix | 69-74 | 6 | |
| β-strand | 79 | 1 | 10 |
| β-strand | 83-85 | 3 | 8 |
| β-strand | 91 | 1 | 9 |
| β-strand | 99 | 1 | 10 |
| α-helix | 102-109 | 8 | |
| β-strand | 112-119 | 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 | 202-206 | 5 | 14 |
| β-strand | 209-213 | 5 | 14 |
| α-helix | 220-222 | 3 | |
| 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 | 7 | 10 |
| β-strand | 268-270 | 3 | 8 |
| β-strand | 274-280 | 7 | 7 |
| β-strand | 282-284 | 3 | 16 |
| β-strand | 287-289 | 3 | 16 |
| β-strand | 295-296 | 2 | 6 |
| β-strand | 302-306 | 5 | 17 |
| α-helix | 307 | 1 | |
| β-strand | 308-309 | 2 | 6 |
| β-strand | 316-318 | 3 | 5 |
| β-strand | 322 | 1 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 506 | 1 | 18 |
| β-strand | 510 | 1 | 18 |
| β-strand | 514 | 1 | 2 |
| β-strand | 522-528 | 7 | 1 |
| β-strand | 531-536 | 6 | 1 |
| α-helix | 538-558 | 21 | |
| β-strand | 562-565 | 4 | 17 |
| α-helix | 575-626 | 52 | |
| α-helix | 627-629 | 3 | |
| β-strand | 630-634 | 5 | 1 |
| β-strand | 637-640 | 4 | 1 |
| α-helix | 646-653 | 8 | |
| α-helix | 659-669 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-6 | 5 | 19 |
| α-helix | 9-21 | 13 | |
| β-strand | 26-30 | 5 | 19 |
| β-strand | 35-39 | 5 | 19 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Hemagglutinin | A | protein | 327 | Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) | P03452 (AlphaFold model) |
| Hemagglutinin | B | protein | 176 | Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) | P03452 (AlphaFold model) |
| Computationally designed peptide HB1.6928.2.3 | C | protein | 40 | synthetic construct |
>5VLI_1 Hemagglutinin (chains A) ADTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAG WLLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPK ESSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIH HPPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTI IFEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTI GECPKYVRSAKLRMVTGLRNIPSIQSR
>5VLI_2 Hemagglutinin (chains B) GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMN IQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYE KVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV
>5VLI_3 Computationally designed peptide HB1.6928.2.3 (chains C) CIEQSFTTLFACQTAAEIWRAFGYTVKIMVDNGNCRLHVC
| ID | Name | Formula | Copies |
|---|---|---|---|
| PGF | 2,5,8,11-tetraoxatridecane | C9 H20 O4 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (PEG) are not listed.
Massively parallel de novo protein design for targeted therapeutics. Chevalier, A., Silva, D.A., Rocklin, G.J. et al. Nature (2017) 550:74-79. DOI 10.1038/nature23912 · 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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