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Crystal structure of a strand-swapped dimer of mouse leukocyte- associated immunoglobulin-like receptor 1 (nysgrc-006047) extra cellular domain
Analyse Crystal structure of a strand-swapped dimer of mouse leukocyte- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ETY
- Type
- protein
- Length
- 386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte-associated immunoglobulin-like receptor 1
- UniProt
- Q8BG84
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 101 | 6% helix, 50% strand | Q8BG84 |
| B | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 93 | 6% helix, 55% strand | Q8BG84 |
| C, D | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 96 | 6% helix, 57% strand | Q8BG84 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.85 | 0.92 | 49 | EDO |
| 2 | 213 | 0.53 | 0.78 | 40 | empty |
| 3 | 116 | 0.53 | 0.82 | 27 | empty |
| 4 | 119 | 0.41 | 0.76 | 27 | empty |
| 5 | 87 | 0.37 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1586 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1565 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 779 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4ETY · Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BG84 · AlphaFold monomer V2.0 prediction for leukocyte-associated immunoglobulin-like receptor 1… · a predicted model of the same protein · chain C 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 Q8BG84
- Elsewhere: RCSB PDB 4ETY · PDBe 4ETY · UniProt Q8BG84
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