MolNFT v1 · #98825 · protein
Crystal structure of D3D4 domain of the LILRB1 molecule
4LL9 · Leukocyte immunoglobulin-like receptor subfamily B member 1: “Crystal structure of D3D4 domain of the LILRB1 molecule”. X-ray diffraction, 1 ligand (IOD), 7 pockets (best druggability 0.64). MolNFT v1 #98825 on GenesisL1: 3D…
- PDB
- 4LL9
- Type
- protein
- Length
- 586 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte immunoglobulin-like receptor subfamily B member 1
- UniProt
- Q8NHL6
- Ligands
- IOD
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 194 | 3% helix, 49% strand | Q8NHL6 |
| B, C | Leukocyte immunoglobulin-like receptor subfamily B member 1 | protein | 196 | 3% helix, 45% strand | Q8NHL6 |
Ligands and binding sites
- IOD · Iodide ion · ion · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.64 | 0.76 | 56 | IOD |
| 2 | 332 | 0.56 | 0.75 | 42 | IOD |
| 3 | 245 | 0.51 | 0.75 | 36 | empty |
| 4 | 144 | 0.49 | 0.78 | 25 | empty |
| 5 | 165 | 0.44 | 0.75 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–C · 626 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 579 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4LL9 · Crystal structure of D3D4 domain of the LILRB1 molecule · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NHL6 · AlphaFold monomer V2.0 prediction for leukocyte immunoglobulin-like receptor subfamily B… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q8NHL6
- Elsewhere: RCSB PDB 4LL9 · PDBe 4LL9 · UniProt Q8NHL6
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