Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate. Determined by X-ray diffraction at 1.9 Å resolution. Released 2 Oct 2019.
Explore 6RTW in 3D Show helices and sheets RCSB PDB PDBe
6RTW contains 19 α-helices and 30 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 | 155-162 | 8 | 1 |
| α-helix | 172-186 | 15 | |
| β-strand | 189-192 | 4 | 2 |
| β-strand | 195-198 | 4 | 2 |
| α-helix | 199-202 | 4 | |
| β-strand | 203 | 1 | 3 |
| β-strand | 205-210 | 6 | 4 |
| α-helix | 214-223 | 10 | |
| α-helix | 225-226 | 2 | |
| β-strand | 228-229 | 2 | 1 |
| α-helix | 231-234 | 4 | |
| α-helix | 236-241 | 6 | |
| β-strand | 246 | 1 | 5 |
| α-helix | 252-253 | 2 | |
| β-strand | 254 | 1 | 5 |
| α-helix | 261-269 | 9 | |
| α-helix | 276-285 | 10 | |
| α-helix | 295-296 | 2 | |
| α-helix | 316-317 | 2 | |
| α-helix | 319-323 | 5 | |
| β-strand | 327-328 | 2 | 6 |
| β-strand | 336-337 | 2 | 6 |
| α-helix | 339-342 | 4 | |
| β-strand | 343-344 | 2 | 1 |
| β-strand | 347-348 | 2 | 7 |
| β-strand | 354-356 | 3 | 7 |
| β-strand | 359-365 | 7 | 1 |
| β-strand | 366 | 1 | 3 |
| α-helix | 367-368 | 2 | |
| α-helix | 369-376 | 8 | |
| α-helix | 380-382 | 3 | |
| α-helix | 389-409 | 21 | |
| β-strand | 417-422 | 6 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-7 | 5 | 8 |
| β-strand | 10-12 | 3 | 4 |
| β-strand | 18-20 | 3 | 9 |
| β-strand | 21-25 | 5 | 8 |
| β-strand | 34-39 | 6 | 4 |
| β-strand | 46-51 | 6 | 4 |
| β-strand | 57-59 | 3 | 4 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-69 | 3 | 9 |
| β-strand | 72 | 1 | 8 |
| β-strand | 77 | 1 | 8 |
| β-strand | 80-82 | 3 | 9 |
| α-helix | 87-89 | 3 | |
| β-strand | 91-101 | 11 | 4 |
| β-strand | 103-110 | 8 | 4 |
| β-strand | 114-118 | 5 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Protein patched homolog 1 | A | protein | 297 | Homo sapiens | Q13635 (AlphaFold model) |
| Llama-derived nanobody NB64 | B | protein | 130 | Lama glama |
>6RTW_1 Protein patched homolog 1 (chains A) ETGELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNR QWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLR WTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTK PLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEH FKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVLSFTGTKHHHHHH
>6RTW_2 Llama-derived nanobody NB64 (chains B) QVQLQESGGGLVQPGGSLRLSCAASGSGNSINVMGWYRQAPGKPRELVAEITSSGTTNYA DSVKGRFSISRDNAKNTVPLQMNSLKPEDTAIYYCSAVLVRFGGLRRSYWGQGTQVTVSS HHHHHHEPEA
| ID | Name | Formula | Copies |
|---|---|---|---|
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 3 |
The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism. Rudolf, A.F., Kinnebrew, M., Kowatsch, C. et al. Nat Chem Biol (2019) 15:975-982. DOI 10.1038/s41589-019-0370-y · PubMed
Other PDB entries of the same protein (UniProt Q13635 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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