Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64). Determined by X-ray diffraction at 2.03 Å resolution. Released 1 Jan 2020.
Explore 6GWN in 3D Show helices and sheets RCSB PDB PDBe
6GWN contains 18 α-helices and 38 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 |
|---|---|---|---|
| α-helix | 6-26 | 21 | |
| β-strand | 32-34 | 3 | 1 |
| α-helix | 36-49 | 14 | |
| α-helix | 52-62 | 11 | |
| α-helix | 71-82 | 12 | |
| β-strand | 91-100 | 10 | 2 |
| α-helix | 104-106 | 3 | |
| α-helix | 109-117 | 9 | |
| β-strand | 122-124 | 3 | 2 |
| α-helix | 129-142 | 14 | |
| β-strand | 163-171 | 9 | 2 |
| β-strand | 175 | 1 | 3 |
| α-helix | 178-180 | 3 | |
| α-helix | 181-183 | 3 | |
| β-strand | 185-190 | 6 | 1 |
| β-strand | 196-214 | 19 | 1 |
| β-strand | 220-227 | 8 | 1 |
| β-strand | 228 | 1 | 3 |
| β-strand | 233-240 | 8 | 1 |
| α-helix | 248-251 | 4 | |
| α-helix | 256-264 | 9 | |
| β-strand | 267-276 | 10 | 1 |
| β-strand | 278-285 | 8 | 2 |
| α-helix | 287-292 | 6 | |
| α-helix | 297-299 | 3 | |
| β-strand | 319-328 | 10 | 2 |
| β-strand | 351-353 | 3 | 1 |
| β-strand | 358-364 | 7 | 1 |
| β-strand | 369-376 | 8 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-7 | 5 | 4 |
| β-strand | 10-12 | 3 | 5 |
| β-strand | 18-25 | 8 | 4 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 5 |
| β-strand | 46-51 | 6 | 5 |
| β-strand | 58-60 | 3 | 5 |
| β-strand | 68-73 | 6 | 4 |
| β-strand | 78-83 | 6 | 4 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-100 | 9 | 5 |
| β-strand | 103-106 | 4 | 5 |
| β-strand | 110-114 | 5 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-7 | 5 | 6 |
| β-strand | 10-12 | 3 | 7 |
| β-strand | 18-25 | 8 | 6 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 7 |
| β-strand | 46-51 | 6 | 7 |
| β-strand | 58-60 | 3 | 7 |
| β-strand | 68-73 | 6 | 6 |
| β-strand | 78-83 | 6 | 6 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 7 |
| α-helix | 108 | 1 | |
| β-strand | 110-111 | 2 | 7 |
| β-strand | 115-119 | 5 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Plasminogen activator inhibitor 1 | A | protein | 379 | Homo sapiens | P05121 (AlphaFold model) |
| VHH-2g-42 | B | protein | 116 | Vicugna pacos | |
| VHH-2w-64 | C | protein | 121 | Vicugna pacos |
>6GWN_1 Plasminogen activator inhibitor 1 (chains A) VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQA AMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRST VKQVDFSEVERARFIINDWVKTHTKGMISNLLGKGAVDQLTRLVLVNALYFNGQFKTPFP DSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAP YEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFR QFQADFTSLSDQEPLHVAQALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIMDRPFLF VVRHNPTGTVLFMGQVMEP
>6GWN_2 VHH-2g-42 (chains B) QVQLVESGGGLVQPGGRLRLSCAASGFTFRTYAMQWYRQSPGTERELVAAISNIGGVTDY GDSVKGRFTISRDNAKTTVYLEMNSLKPEDTATYYCSAVRLPQRYWGRGTQVTVSS
>6GWN_3 VHH-2w-64 (chains C) QVQLVESGGGLVQAGGSLRLSCAASGFTFDDYSIAWFRQAPGKEREGVSCISSSDGSAYY ADSVKGRFTISSDNAKNTVYLQMNSLKPEDTAVYYCAAVWARVCRNPYDYWGQGTQVTVS S
Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction. Sillen, M., Weeks, S.D., Zhou, X. et al. J Thromb Haemost (2020) 18:681-692. DOI 10.1111/jth.14716 · PubMed
Other PDB entries of the same protein (UniProt P05121 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 6GWN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.