Research workbench
Crystal structure of sonic hedgehog bound to the third fniii domain of cdo
Analyse Crystal structure of sonic hedgehog bound to the third fniii domain of cdo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D1M
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sonic hedgehog protein; Cell adhesion molecule
- UniProt
- Q62226, Q4KMG0
- Ligands
- CA, ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sonic hedgehog protein | protein | 148 | 28% helix, 21% strand | Q62226 |
| B | Sonic hedgehog protein | protein | 150 | 27% helix, 21% strand | Q62226 |
| C | Cell adhesion molecule | protein | 87 | 0% helix, 54% strand | Q4KMG0 |
| D | Cell adhesion molecule | protein | 99 | 7% helix, 45% strand | Q4KMG0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.55 | 0.77 | 37 | empty |
| 2 | 238 | 0.50 | 0.75 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–C · 714 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 693 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 394 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3D1M · Crystal Structure of Sonic Hedgehog Bound to the third FNIII domain of CDO · the same entry in another collection · chain D against D, TM-score 1.00
- Q62226 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q62226) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q4KMG0 · AlphaFold monomer V2.0 prediction for cell adhesion molecule- RELATED/DOWN-regulated by… · a predicted model of the same protein · chain D 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 Q62226
- Every structure of UniProt Q4KMG0
- Elsewhere: RCSB PDB 3D1M · PDBe 3D1M · UniProt Q62226 · UniProt Q4KMG0
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