Research workbench
Cryo-EM structure of the 2:1 hPtch1-Shhp complex
Analyse Cryo-EM structure of the 2:1 hPtch1-Shhp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7H
- Type
- protein
- Length
- 2,153 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens
- Molecule
- Protein patched homolog 1; Sonic hedgehog protein
- UniProt
- Q13635, Q15465
- Ligands
- CLR, PLM, NAG, CA, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.6 · 3 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 991 | 53% helix, 6% strand | Q13635 |
| B | Protein patched homolog 1 | protein | 988 | 52% helix, 5% strand | Q13635 |
| C | Sonic hedgehog protein | protein | 174 | 20% helix, 15% strand | Q15465 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A, B, C
- PLM · Palmitic acid · ligand · chains B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.88 | 0.93 | 74 | CLR |
| 2 | 370 | 0.86 | 0.94 | 52 | PLM |
| 3 | 363 | 0.84 | 0.92 | 46 | CLR |
| 4 | 915 | 0.82 | 0.83 | 76 | CLR |
| 5 | 319 | 0.79 | 0.90 | 40 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2314 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1217 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 6 disulfide, 2 covalent, 2 lipid (N-glycosylation, disulfide, covalent ligand, palmitoylation).
Compared structures
- 6N7H · Cryo-EM structure of the 2:1 HPTCH1-shhp 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 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 6N7H · PDBe 6N7H · UniProt Q13635 · UniProt Q15465
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