Research workbench
Crystal structure of leucine-rich repeat domain of APL1B
Analyse Crystal structure of leucine-rich repeat domain of APL1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XGO
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anopheles plasmodium-responsive leucine-rich repeat protein 1B
- UniProt
- F2YBL9
- Ligands
- NAG, NA, PO4, CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anopheles plasmodium-responsive leucine-rich repeat protein 1B | protein | 340 | 11% helix, 21% strand | F2YBL9 |
| B | Anopheles plasmodium-responsive leucine-rich repeat protein 1B | protein | 328 | 11% helix, 21% strand | F2YBL9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A
- ACT · Acetate ion · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.51 | 0.79 | 19 | empty |
| 2 | 67 | 0.29 | 0.73 | 14 | empty |
| 3 | 71 | 0.29 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1529 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4XGO · Crystal structure of leucine-rich repeat domain of APL1B · 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 F2YBL9
- Elsewhere: RCSB PDB 4XGO · PDBe 4XGO · UniProt F2YBL9
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