Research workbench
Cryo-EM structure of murine dispatched in complex with sonic hedgehog
Analyse Cryo-EM structure of murine dispatched in complex with sonic hedgehog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RPK
- Type
- protein
- Length
- 1,104 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein dispatched homolog 1; Sonic hedgehog protein
- UniProt
- Q3TDN0, Q62226
- Ligands
- Y01, AV0, 6OE, NAG, NA, CA, ZN, SO4
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 2 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dispatched homolog 1 | protein | 953 | 60% helix, 7% strand | Q3TDN0 |
| H | Sonic hedgehog protein | protein | 151 | 28% helix, 21% strand | Q62226 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 26 copies · chains A
- AV0 · 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 2 copies · chains A
- 6OE · (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains H
- ZN · Zinc ion · metal · chains H
- SO4 · Sulfate ion · ion · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.98 | 21 | empty |
| 2 | 390 | 0.66 | 0.80 | 45 | empty |
| 3 | 186 | 0.64 | 0.84 | 27 | empty |
| 4 | 149 | 0.59 | 0.83 | 21 | empty |
| 5 | 205 | 0.59 | 0.81 | 33 | empty |
Interfaces
1 interface between chains.
- A–H · 1096 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7RPK · Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog · the same entry in another collection · chain A against A, TM-score 1.00
- Q62226 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q62226) · a predicted model of the same protein · chain H against A, TM-score 0.99
- Q3TDN0 · AlphaFold monomer V2.0 prediction for protein dispatched homolog 1 (Q3TDN0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q3TDN0
- Every structure of UniProt Q62226
- Elsewhere: RCSB PDB 7RPK · PDBe 7RPK · UniProt Q3TDN0 · UniProt Q62226
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