MolNFT v1 · #125128 · protein
Crystal structure of the xenopus smoothened cysteine-rich domain (crd) in complex with 20(S)-hydroxycholesterol
5KZV: “Crystal structure of the xenopus smoothened cysteine-rich domain (crd) in complex with…”. X-ray diffraction, 1 ligand (HCD), 2 pockets (best druggability 0.31). MolNFT v1 #125128 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5KZV
- Type
- protein
- Length
- 117 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened
- UniProt
- Q98SW5
- Ligands
- HCD
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened | protein | 117 | 38% helix, 14% strand | Q98SW5 |
Ligands and binding sites
- HCD · (3alpha,8alpha)-cholest-5-ene-3,20-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.31 | 0.72 | 14 | HCD |
| 2 | 64 | 0.29 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5KZV · 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 5KZV · PDBe 5KZV · UniProt Q98SW5
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