MolNFT v1 · #145953 · protein
Crystal structure of xenopus smoothened in complex with cyclopamine
6D32 · SMOOTHENED,SOLUBLE cytochrome B562,SMOOTHENED: “Crystal structure of xenopus smoothened in complex with cyclopamine”. X-ray diffraction, 1 ligand (CY8), 7 pockets (best druggability 0.86). MolNFT v1 #145953 on GenesisL1: 3D…
- PDB
- 6D32
- Type
- protein
- Length
- 573 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SMOOTHENED,SOLUBLE cytochrome B562,SMOOTHENED
- UniProt
- Q98SW5, P0ABE7
- Ligands
- CY8
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SMOOTHENED,SOLUBLE cytochrome B562,SMOOTHENED | protein | 573 | 63% helix, 6% strand | Q98SW5, P0ABE7 |
Ligands and binding sites
- CY8 · Cyclopamine · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.86 | 0.89 | 81 | CY8 |
| 2 | 224 | 0.50 | 0.75 | 30 | empty |
| 3 | 58 | 0.34 | 0.77 | 12 | empty |
| 4 | 68 | 0.34 | 0.76 | 16 | empty |
| 5 | 88 | 0.32 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6D32 · Crystal structure of Xenopus Smoothened in complex with cyclopamine · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.17
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
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6D32 · PDBe 6D32 · UniProt Q98SW5 · UniProt P0ABE7
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