Research workbench
Japanin from rhipicephalus appendiculatus bound to cholesterol: orthorhombic crystal form
Analyse Japanin from rhipicephalus appendiculatus bound to cholesterol: orthorhombic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BQU
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Japanin
- UniProt
- M1MR49
- Ligands
- CLR, NAG, FUC, MAN, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Japanin | protein | 152 | 19% helix, 44% strand | M1MR49 |
| B | Japanin | protein | 149 | 15% helix, 44% strand | M1MR49 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.81 | 0.88 | 52 | CLR |
| 2 | 437 | 0.79 | 0.86 | 49 | CLR |
| 3 | 170 | 0.58 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1147 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4BQU · Japanin from Rhipicephalus appendiculatus bound to cholesterol: Orthorhombic 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 4BQU · PDBe 4BQU · UniProt M1MR49
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