MolNFT v1 · #122244 · protein
The crystal structure of mouse TLR4/MD-2/LIPID a complex
5IJD · Toll-like receptor 4, variable lymphocyte receptor B chimera: “The crystal structure of mouse TLR4/MD-2/LIPID a complex”. X-ray diffraction, 5 ligands (LP4, LP5, DAO), 8 pockets (best druggability 0.80). MolNFT v1 #122244 on…
- PDB
- 5IJD
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 4, variable lymphocyte receptor B chimera; Lymphocyte antigen 96
- UniProt
- Q9QUK6, Q4G1L2, Q9JHF9
- Ligands
- LP4, LP5, DAO, MYR, NAG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 4, variable lymphocyte receptor B chimera | protein | 590 | 9% helix, 21% strand | Q9QUK6, Q4G1L2 |
| C, D | Lymphocyte antigen 96 | protein | 137 | 3% helix, 56% strand | Q9JHF9 |
| B | Toll-like receptor 4, variable lymphocyte receptor B chimera | protein | 592 | 7% helix, 20% strand | Q9QUK6, Q4G1L2 |
Ligands and binding sites
- LP4 · 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose · ligand · 2 copies · chains A, C, D, B
- LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · 2 copies · chains C, B, A, D
- DAO · Lauric acid · ligand · 2 copies · chains C, D
- MYR · Myristic acid · ligand · 2 copies · chains A, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.80 | 0.82 | 62 | LP4, LP5, DAO, MYR |
| 2 | 831 | 0.80 | 0.81 | 56 | LP4, LP5, DAO, MYR |
| 3 | 957 | 0.73 | 0.77 | 106 | empty |
| 4 | 694 | 0.72 | 0.78 | 92 | empty |
| 5 | 612 | 0.70 | 0.79 | 51 | empty |
Interfaces
5 interfaces between chains.
- D–B · 1123 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1093 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 456 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5IJD · The crystal structure of mouse TLR4/MD-2/lipid A complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QUK6 · AlphaFold monomer V2.0 prediction for toll-like receptor 4 (Q9QUK6) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9JHF9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9JHF9) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9QUK6
- Every structure of UniProt Q4G1L2
- Every structure of UniProt Q9JHF9
- Elsewhere: RCSB PDB 5IJD · PDBe 5IJD · UniProt Q9QUK6 · UniProt Q4G1L2 · UniProt Q9JHF9
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