MolNFT v1 · #90750 · protein
Crystal structure of a strand-swapped dimer of mouse leukocyte- associated immunoglobulin-like receptor 1 (nysgrc-006047)IG-like domain
4ESK · Leukocyte-associated immunoglobulin-like receptor 1: “Crystal structure of a strand-swapped dimer of mouse leukocyte- associated immunoglobulin-like receptor 1…”. X-ray diffraction, 2 ligands (NA, K), 5 pockets (best druggability…
- PDB
- 4ESK
- 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
- Ligands
- NA, K
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 96 | 6% helix, 56% strand | Q8BG84 |
| C | Leukocyte-associated immunoglobulin-like receptor 1 | protein | 98 | 6% helix, 51% strand | Q8BG84 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, D
- K · Potassium ion · metal · chains B
- GOL · Glycerol · additive · 3 copies · chains B, C, 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 | 460 | 0.85 | 0.92 | 46 | empty |
| 2 | 150 | 0.52 | 0.80 | 28 | empty |
| 3 | 156 | 0.51 | 0.79 | 29 | empty |
| 4 | 109 | 0.42 | 0.77 | 27 | NA |
| 5 | 110 | 0.39 | 0.75 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1623 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1607 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 868 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 863 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4ESK · 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 A against A, TM-score 0.82
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 4ESK · PDBe 4ESK · UniProt Q8BG84
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