Research workbench
Crystal structure of the xenopus smoothened cysteine-rich domain (crd) in complex with cyclopamine
Analyse Crystal structure of the xenopus smoothened cysteine-rich domain (crd) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZY
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened
- UniProt
- Q98SW5
- Ligands
- CY8
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened | protein | 117 | 37% helix, 15% strand | Q98SW5 |
| B | Smoothened | protein | 113 | 42% helix, 11% strand | Q98SW5 |
Ligands and binding sites
- CY8 · Cyclopamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.61 | 0.84 | 31 | empty |
| 2 | 226 | 0.53 | 0.77 | 28 | empty |
| 3 | 107 | 0.38 | 0.74 | 14 | CY8 |
| 4 | 111 | 0.36 | 0.73 | 14 | CY8 |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5KZY · Crystal structure of the xenopus Smoothened cysteine-rich domain (CRD) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q98SW5
- Elsewhere: RCSB PDB 5KZY · PDBe 5KZY · UniProt Q98SW5
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