Research workbench
Structure of PTCH1 bound to a modified hedgehog ligand shhn-C24II
Analyse Structure of PTCH1 bound to a modified hedgehog ligand shhn-C24II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RMG
- Type
- protein
- Length
- 1,176 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related; Sonic…
- UniProt
- Q13635, U6GSR1, Q15465
- Ligands
- Y01, NAG, ZN
- Pockets
- 12 · best druggability 0.90
Structure
electron microscopy · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related | protein | 1026 | 54% helix, 7% strand | Q13635, U6GSR1 |
| B | Sonic hedgehog protein | protein | 150 | 24% helix, 15% strand | Q15465 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 11 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.90 | 0.92 | 129 | Y01 |
| 2 | 432 | 0.79 | 0.87 | 55 | empty |
| 3 | 314 | 0.71 | 0.84 | 30 | empty |
| 4 | 65 | 0.64 | 0.92 | 22 | empty |
| 5 | 364 | 0.61 | 0.77 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1230 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6RMG · Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II · 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 U6GSR1
- Every structure of UniProt Q15465
- Elsewhere: RCSB PDB 6RMG · PDBe 6RMG · UniProt Q13635 · UniProt U6GSR1 · UniProt Q15465
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