Research workbench
Cryo-EM structure of human PTCH1 and shhn complex
Analyse Cryo-EM structure of human PTCH1 and shhn complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DMY
- Type
- protein
- Length
- 1,143 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Sonic hedgehog protein
- UniProt
- Q13635, Q15465
- Ligands
- Y01, SER, NAG, CA, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 992 | 51% helix, 5% strand | Q13635 |
| B | Sonic hedgehog protein | protein | 151 | 20% helix, 15% strand | Q15465 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A
- SER · Serine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.87 | 0.93 | 79 | empty |
| 2 | 397 | 0.86 | 0.94 | 55 | Y01 |
| 3 | 437 | 0.79 | 0.87 | 46 | CA |
| 4 | 148 | 0.70 | 0.90 | 26 | empty |
| 5 | 57 | 0.70 | 0.97 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1183 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 6DMY · Cryo-EM structure of human Ptch1 and ShhN complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q13635 · AlphaFold monomer V2.0 prediction for protein patched homolog 1 (Q13635) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q13635
- Every structure of UniProt Q15465
- Elsewhere: RCSB PDB 6DMY · PDBe 6DMY · UniProt Q13635 · UniProt Q15465
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