Short PCSK9 delta-P' complex with shrunken peptide bearing homo-Arginine. Determined by X-ray diffraction at 2.2 Å resolution. Released 16 Aug 2017.
Explore 5VLK in 3D Show helices and sheets RCSB PDB PDBe
5VLK contains 17 α-helices and 27 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 | 63-65 | 3 | 1 |
| α-helix | 70-72 | 3 | |
| β-strand | 73-82 | 10 | 1 |
| α-helix | 83 | 1 | |
| α-helix | 88-104 | 17 | |
| β-strand | 110-115 | 6 | 1 |
| β-strand | 121-125 | 5 | 1 |
| α-helix | 128-130 | 3 | |
| α-helix | 131-135 | 5 | |
| β-strand | 140-147 | 8 | 1 |
| β-strand | 148-151 | 4 | 2 |
| β-strand | 181-186 | 6 | 3 |
| β-strand | 200-206 | 7 | 3 |
| α-helix | 209-211 | 3 | |
| α-helix | 225-235 | 11 | |
| β-strand | 246-251 | 6 | 3 |
| β-strand | 258-260 | 3 | 2 |
| α-helix | 261-277 | 17 | |
| β-strand | 283-287 | 5 | 3 |
| β-strand | 289-292 | 4 | 2 |
| α-helix | 295-306 | 12 | |
| β-strand | 310-314 | 5 | 3 |
| β-strand | 318 | 1 | 4 |
| β-strand | 321 | 1 | 5 |
| α-helix | 322-324 | 3 | |
| β-strand | 325-326 | 2 | 2 |
| β-strand | 334-339 | 6 | 3 |
| β-strand | 345 | 1 | 3 |
| α-helix | 346 | 1 | |
| β-strand | 347-348 | 2 | 4 |
| β-strand | 351-352 | 2 | 4 |
| β-strand | 355 | 1 | 5 |
| β-strand | 361-364 | 4 | 3 |
| β-strand | 368-371 | 4 | 6 |
| β-strand | 379-382 | 4 | 6 |
| α-helix | 385-402 | 18 | |
| α-helix | 408-418 | 11 | |
| β-strand | 420-421 | 2 | 3 |
| α-helix | 426-428 | 3 | |
| α-helix | 431-433 | 3 | |
| β-strand | 440-441 | 2 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 6 |
| α-helix | 6-12 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 2-5 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Proprotein convertase subtilisin/kexin type 9 | A | protein | 460 | Homo sapiens | Q8NBP7 (AlphaFold model) |
| Ace-thr-val-phe-thr-ser-trp-glu-glu-tyr-leu-asp-trp-val-NH2 peptide | Y | protein | 15 | synthetic construct | |
| ACE-TRP-ASN-LEU-VAL-HRG-ILE-GLY-LEU-LEU peptide | Z | protein | 11 | synthetic construct |
>5VLK_1 Proprotein convertase subtilisin/kexin type 9 (chains A) MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGT TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLP GFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYSADEYQPPDGGSLV EVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAG VAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAA CQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVD LFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSA KDVINEAWFPEDQRVLTPNLVAALPPSTHGAGNSHHHHHH
>5VLK_2 ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2 peptide (chains Y) XTVFTSWEEYLDWVX
>5VLK_3 ACE-TRP-ASN-LEU-VAL-HRG-ILE-GLY-LEU-LEU peptide (chains Z) XWNLVRIGLLR
| ID | Name | Formula | Copies |
|---|---|---|---|
| CA | Calcium ion | Ca | 1 |
Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists. Zhang, Y., Ultsch, M., Skelton, N.J. et al. Nat Struct Mol Biol (2017) 24:848-856. DOI 10.1038/nsmb.3453 · PubMed
Other PDB entries of the same protein (UniProt Q8NBP7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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