Research workbench
Revised cryo-EM structure of the human 2:1 PTCH1-shh complex
Analyse Revised cryo-EM structure of the human 2:1 PTCH1-shh complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RVD
- Type
- protein
- Length
- 2,138 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Sonic hedgehog protein
- UniProt
- Q13635, Q15465
- Ligands
- CLR, PLM, NAG, CA, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 986 | 56% helix, 8% strand | Q13635 |
| B | Protein patched homolog 1 | protein | 978 | 56% helix, 8% strand | Q13635 |
| C | Sonic hedgehog protein | protein | 174 | 24% helix, 18% strand | Q15465 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C
- PLM · Palmitic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.87 | 0.93 | 61 | CLR |
| 2 | 256 | 0.84 | 0.95 | 39 | PLM |
| 3 | 810 | 0.84 | 0.86 | 69 | empty |
| 4 | 928 | 0.83 | 0.84 | 83 | CLR |
| 5 | 699 | 0.80 | 0.84 | 91 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2237 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1280 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 5 disulfide, 1 covalent, 1 lipid (N-glycosylation, disulfide, covalent ligand, palmitoylation).
Compared structures
- 6RVD · Revised cryo-EM structure of the human 2:1 Ptch1-Shh 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 B 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 6RVD · PDBe 6RVD · UniProt Q13635 · UniProt Q15465
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