MolNFT v1 · #87026 · protein
Japanin from rhipicephalus appendiculatus bound to cholesterol: tetragonal crystal form
4BOE: “Japanin from rhipicephalus appendiculatus bound to cholesterol: tetragonal crystal form”. X-ray diffraction, 4 ligands (CLR, NAG, MAN), 1 pocket (best druggability 0.82). MolNFT v1 #87026 on GenesisL1: 3D structure, binding sites…
- PDB
- 4BOE
- Type
- protein
- Length
- 154 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Japanin
- UniProt
- M1MR49
- Ligands
- CLR, NAG, MAN, FUC
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Japanin | protein | 154 | 18% helix, 42% strand | M1MR49 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
- IMD · Imidazole · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.82 | 0.89 | 59 | CLR, MPD |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4BOE · Japanin from Rhipicephalus appendiculatus bound to cholesterol: Tetragonal crystal form · 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 M1MR49
- Elsewhere: RCSB PDB 4BOE · PDBe 4BOE · UniProt M1MR49
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