Research workbench
Crystal structure of plant glycosylphosphatidylinositol-anchored protein LLG1
Analyse Crystal structure of plant glycosylphosphatidylinositol-anchored protein LLG1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A5D
- Type
- protein
- Length
- 186 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gpi-anchored protein LLG1
- UniProt
- Q9FKT1
- Ligands
- FUC, NAG
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gpi-anchored protein LLG1 | protein | 93 | 51% helix, 4% strand | Q9FKT1 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.65 | 0.84 | 30 | FUC |
| 2 | 376 | 0.60 | 0.77 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 417 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6A5D · Crystal structure of plant Glycosylphosphatidylinositol-anchored Protein LLG1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FKT1 · AlphaFold monomer V2.0 prediction for gpi-anchored protein LLG1 (Q9FKT1) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 Q9FKT1
- Elsewhere: RCSB PDB 6A5D · PDBe 6A5D · UniProt Q9FKT1
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