Research workbench
Cryo-EM structure of HDISP1NNN-shhn
Analyse Cryo-EM structure of HDISP1NNN-shhn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E2I
- Type
- protein
- Length
- 1,058 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sonic hedgehog protein; Protein dispatched homolog 1
- UniProt
- Q15465, Q96F81
- Ligands
- Y01, NAG, ZN
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Sonic hedgehog protein | protein | 151 | 25% helix, 17% strand | Q15465 |
| D | Protein dispatched homolog 1 | protein | 907 | 54% helix, 4% strand | Q96F81 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 7 copies · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D
- ZN · Zinc ion · metal · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.72 | 0.94 | 24 | empty |
| 2 | 689 | 0.70 | 0.77 | 69 | empty |
| 3 | 262 | 0.69 | 0.84 | 46 | empty |
| 4 | 204 | 0.68 | 0.86 | 37 | empty |
| 5 | 50 | 0.66 | 0.96 | 17 | empty |
Interfaces
1 interface between chains.
- G–D · 866 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 7E2I · Cryo-EM structure of hDisp1NNN-ShhN · the same entry in another collection · chain G against G, TM-score 1.00
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain G against A, TM-score 0.96
- Q96F81 · AlphaFold monomer V2.0 prediction for protein dispatched homolog 1 (Q96F81) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q15465
- Every structure of UniProt Q96F81
- Elsewhere: RCSB PDB 7E2I · PDBe 7E2I · UniProt Q15465 · UniProt Q96F81
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