Research workbench
Crystal structure sonic hedgehog bound to the 5E1 Fab fragment
Analyse Crystal structure sonic hedgehog bound to the 5E1 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MXW
- Type
- protein
- Length
- 585 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sonic hedgehog protein; 5E1 light chain; 5E1 heavy chain
- UniProt
- Q15465
- Ligands
- CA, ZN, SO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sonic hedgehog protein | protein | 153 | 29% helix, 20% strand | Q15465 |
| L | 5E1 light chain | protein | 212 | 6% helix, 52% strand | — |
| H | 5E1 heavy chain | protein | 220 | 10% helix, 52% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, H
- SO4 · Sulfate ion · ion · 3 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.63 | 0.74 | 80 | empty |
| 2 | 55 | 0.55 | 0.90 | 20 | empty |
| 3 | 121 | 0.50 | 0.81 | 23 | empty |
| 4 | 158 | 0.47 | 0.76 | 25 | SO4 |
| 5 | 72 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1853 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 526 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 465 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 3MXW · PDBe 3MXW · UniProt Q15465
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