Research workbench
Structure of 2:1 human PTCH1-shh-N complex
Analyse Structure of 2:1 human PTCH1-shh-N complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E1H
- Type
- protein
- Length
- 2,120 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Sonic hedgehog protein N-product
- UniProt
- Q13635, Q15465
- Ligands
- PLM, CA, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein patched homolog 1 | protein | 978 | 53% helix, 6% strand | Q13635 |
| C | Sonic hedgehog protein N-product | protein | 164 | 22% helix, 13% strand | Q15465 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A, C
- CA · Calcium ion · metal · 2 copies · chains C
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.86 | 0.87 | 96 | empty |
| 2 | 249 | 0.84 | 0.95 | 37 | PLM |
| 3 | 1064 | 0.84 | 0.85 | 93 | empty |
| 4 | 656 | 0.79 | 0.84 | 67 | empty |
| 5 | 386 | 0.79 | 0.88 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2059 Ų buried · 23 hydrogen bonds · protein-protein
- C–B · 1326 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 6E1H · Structure of 2:1 human Ptch1-Shh-N 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 0.97
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 6E1H · PDBe 6E1H · UniProt Q13635 · UniProt Q15465
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