Research workbench
3.0A syn structure of the multi-domain human smoothened receptor in complex with TC114
Analyse 3.0A syn structure of the multi-domain human smoothened receptor in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V57
- Type
- protein
- Length
- 1,286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened HOMOLOG,FLAVODOXIN,SMOOTHENED homolog
- UniProt
- Q99835, P00323
- Ligands
- 836, FMN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened HOMOLOG,FLAVODOXIN,SMOOTHENED homolog | protein | 645 | 52% helix, 11% strand | Q99835, P00323 |
| B | Smoothened HOMOLOG,FLAVODOXIN,SMOOTHENED homolog | protein | 641 | 52% helix, 12% strand | Q99835, P00323 |
Ligands and binding sites
- 836 · N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl) benzamide · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.81 | 0.90 | 49 | 836 |
| 2 | 380 | 0.81 | 0.90 | 48 | 836 |
| 3 | 53 | 0.71 | 0.98 | 21 | empty |
| 4 | 663 | 0.68 | 0.77 | 56 | empty |
| 5 | 118 | 0.50 | 0.80 | 22 | FMN |
Interfaces
1 interface between chains.
- A–B · 765 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5V57 · 3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114 · the same entry in another collection · chain A against A, TM-score 1.00
- Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain A against A, TM-score 0.75
- P00323 · AlphaFold monomer V2.0 prediction for flavodoxin (P00323) · a predicted model of the same protein · chain B against A, TM-score 0.23
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 Q99835
- Every structure of UniProt P00323
- Elsewhere: RCSB PDB 5V57 · PDBe 5V57 · UniProt Q99835 · UniProt P00323
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