Research workbench
Structure of human PATCHED1 in complex with native sonic hedgehog
Analyse Structure of human PATCHED1 in complex with native sonic hedgehog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OEV
- Type
- protein
- Length
- 1,129 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
- PLM, NAG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 964 | 56% helix, 5% strand | Q13635 |
| C | Sonic hedgehog protein | protein | 165 | 21% helix, 13% strand | Q15465 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.82 | 0.96 | 31 | PLM |
| 2 | 700 | 0.78 | 0.83 | 61 | empty |
| 3 | 269 | 0.75 | 0.88 | 40 | empty |
| 4 | 748 | 0.74 | 0.79 | 70 | empty |
| 5 | 339 | 0.70 | 0.83 | 32 | empty |
Interfaces
1 interface between chains.
- A–C · 1731 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (palmitoylation).
Compared structures
- 6OEV · Structure of human Patched1 in complex with native Sonic Hedgehog · 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 0.98
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 6OEV · PDBe 6OEV · UniProt Q13635 · UniProt Q15465
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