Cryo-EM structure of human Ptch1 and ShhN complex. Determined by electron microscopy at 3.6 Å resolution. Released 11 Jul 2018.
Explore 6DMY in 3D Show helices and sheets RCSB PDB PDBe
6DMY contains 51 α-helices and 25 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 | 75-95 | 21 | |
| α-helix | 98-114 | 17 | |
| β-strand | 121 | 1 | 1 |
| α-helix | 137-143 | 7 | |
| β-strand | 156-161 | 6 | 2 |
| α-helix | 172-184 | 13 | |
| β-strand | 190 | 1 | 3 |
| β-strand | 197 | 1 | 3 |
| α-helix | 199-202 | 4 | |
| α-helix | 215-222 | 8 | |
| β-strand | 228-229 | 2 | 2 |
| α-helix | 231-233 | 3 | |
| α-helix | 261-266 | 6 | |
| α-helix | 276-284 | 9 | |
| β-strand | 326-328 | 3 | 4 |
| β-strand | 336-338 | 3 | 4 |
| α-helix | 339-342 | 4 | |
| β-strand | 348 | 1 | 5 |
| β-strand | 354 | 1 | 5 |
| β-strand | 360-364 | 5 | 2 |
| α-helix | 369-375 | 7 | |
| α-helix | 389-409 | 21 | |
| β-strand | 418-422 | 5 | 2 |
| α-helix | 426-434 | 9 | |
| α-helix | 439-456 | 18 | |
| α-helix | 467-488 | 22 | |
| β-strand | 495 | 1 | 1 |
| α-helix | 499-524 | 26 | |
| α-helix | 536-542 | 7 | |
| α-helix | 545-563 | 19 | |
| α-helix | 568-604 | 37 | |
| α-helix | 731-734 | 4 | |
| α-helix | 741-744 | 4 | |
| α-helix | 751-768 | 18 | |
| β-strand | 773 | 1 | 6 |
| α-helix | 782 | 1 | |
| α-helix | 786-794 | 9 | |
| β-strand | 801-808 | 8 | 7 |
| α-helix | 817-825 | 9 | |
| α-helix | 826-829 | 4 | |
| α-helix | 841-843 | 3 | |
| α-helix | 844-862 | 19 | |
| α-helix | 882-888 | 7 | |
| α-helix | 899-903 | 5 | |
| α-helix | 921-929 | 9 | |
| α-helix | 931-936 | 6 | |
| α-helix | 944-947 | 4 | |
| α-helix | 966-968 | 3 | |
| β-strand | 972-978 | 7 | 7 |
| α-helix | 984-1001 | 18 | |
| β-strand | 1007-1012 | 6 | 7 |
| α-helix | 1013-1017 | 5 | |
| α-helix | 1027-1045 | 19 | |
| α-helix | 1050-1074 | 25 | |
| β-strand | 1078 | 1 | 6 |
| α-helix | 1082-1106 | 25 | |
| α-helix | 1113-1121 | 9 | |
| α-helix | 1123-1140 | 18 | |
| α-helix | 1146-1148 | 3 | |
| α-helix | 1149-1153 | 5 | |
| α-helix | 1154-1163 | 10 | |
| α-helix | 1164-1170 | 7 | |
| α-helix | 1171-1177 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 41-43 | 3 | |
| β-strand | 47-48 | 2 | 8 |
| α-helix | 71-73 | 3 | |
| β-strand | 77 | 1 | 9 |
| β-strand | 85-86 | 2 | 8 |
| β-strand | 98 | 1 | 9 |
| α-helix | 100-114 | 15 | |
| β-strand | 123-126 | 4 | 8 |
| α-helix | 139-141 | 3 | |
| β-strand | 145-149 | 5 | 8 |
| α-helix | 158-166 | 9 | |
| β-strand | 172-174 | 3 | 8 |
| β-strand | 181-184 | 4 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Protein patched homolog 1 | A | protein | 1349 | Homo sapiens | Q13635 (AlphaFold model) |
| Sonic hedgehog protein | B | protein | 177 | Homo sapiens | Q15465 (AlphaFold model) |
>6DMY_1 Protein patched homolog 1 (chains A) MADYKDDDDKSGPDEVDASGRMASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGL RRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCG KFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMI QTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQI IEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWE EMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQE ELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAW QRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLR WDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLA HAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAV VVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRY SPPPPYSSHSFAHETQITMQSTVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSC QSPESTSSTRDLLSQFSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLG LLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLL YDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDD GVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQA NIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICS NYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMV LALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLAL EHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFG PYPEVSPANGLNRLPTPSPEPPPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELR HYEAQQGAGGPAHQVIVEATENPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQG QQPRRDLEGSDEVDAVEGSHHHHHHHHHH
>6DMY_2 Sonic hedgehog protein (chains B) AHMCGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNY NPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLH YEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 5 |
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 2 |
| SER | Serine | C3 H7 N O3 | 1 |
| ZN | Zinc ion | Zn | 1 |
| CA | Calcium ion | Ca | 2 |
Structural basis for the recognition of Sonic Hedgehog by human Patched1. Gong, X., Qian, H., Cao, P. et al. Science (2018) 361. DOI 10.1126/science.aas8935 · 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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