MolNFT v1 · #92445 · protein
Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with md-2 and lps
4G8A · Toll-like receptor 4: “Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with md-2 and lps”. X-ray diffraction, 6 ligands (LP4, LP5, DAO), 10 pockets (best druggability 0.80). MolNFT v1 #92445 on…
- PDB
- 4G8A
- Type
- protein
- Length
- 1,486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 4; Lymphocyte antigen 96
- UniProt
- O00206, Q9Y6Y9
- Ligands
- LP4, LP5, DAO, MYR, NAG, KDO
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 4 | protein | 601 | 11% helix, 24% strand | O00206 |
| B | Toll-like receptor 4 | protein | 605 | 10% helix, 24% strand | O00206 |
| C, D | Lymphocyte antigen 96 | protein | 140 | 3% helix, 54% strand | Q9Y6Y9 |
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, B, D
- 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 B, C, 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 · 12 copies · chains A, B, C, D
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.80 | 0.81 | 59 | LP4, LP5, DAO, MYR |
| 2 | 1088 | 0.80 | 0.81 | 76 | LP4, LP5, DAO, MYR |
| 3 | 1020 | 0.75 | 0.78 | 107 | empty |
| 4 | 758 | 0.72 | 0.78 | 78 | empty |
| 5 | 691 | 0.70 | 0.78 | 80 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1088 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1086 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 730 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 533 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4G8A · Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2… · the same entry in another collection · chain A against A, TM-score 1.00
- O00206 · AlphaFold monomer V2.0 prediction for toll-like receptor 4 (O00206) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9Y6Y9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9Y6Y9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O00206
- Every structure of UniProt Q9Y6Y9
- Elsewhere: RCSB PDB 4G8A · PDBe 4G8A · UniProt O00206 · UniProt Q9Y6Y9
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