Research workbench
Crystal structure of human lectin-like oxidized low-density lipoprotein receptor 1 (lox-1) at low pH
Analyse Crystal structure of human lectin-like oxidized low-density lipoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YXJ
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidised low density lipoprotein (lectin-like) receptor 1
- UniProt
- P78380
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidised low density lipoprotein (lectin-like) receptor 1 | protein | 130 | 15% helix, 34% strand | P78380 |
| B | Oxidised low density lipoprotein (lectin-like) receptor 1 | protein | 128 | 16% helix, 34% strand | P78380 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.48 | 0.76 | 26 | empty |
| 2 | 58 | 0.31 | 0.75 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 535 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 modified (disulfide, engineered).
Compared structures
- 1YXJ · Crystal structure of human lectin-like oxidized low-density lipoprotein receptor 1… · the same entry in another collection · chain A against A, TM-score 1.00
- P78380 · AlphaFold monomer V2.0 prediction for oxidized low-density lipoprotein receptor 1 (P78380) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P78380
- Elsewhere: RCSB PDB 1YXJ · PDBe 1YXJ · UniProt P78380
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