Research workbench
Crystal structure of the human TLR4 TV3 hybrid-md-2-eritoran complex
Analyse Crystal structure of the human TLR4 TV3 hybrid-md-2-eritoran complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z65
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 4, variable lymphocyte receptor B; Lymphocyte antigen 96
- UniProt
- O00206, Q4G1L2, Q9Y6Y9
- Ligands
- E55, NAG, BMA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 4, variable lymphocyte receptor B | protein | 276 | 9% helix, 20% strand | O00206, Q4G1L2 |
| C, D | Lymphocyte antigen 96 | protein | 140 | 3% helix, 50% strand | Q9Y6Y9 |
Ligands and binding sites
- E55 · 3-O-decyl-2-deoxy-6-O-{2-deoxy-3-O-[(3R)-3-methoxydecyl]-6-O-methyl-2-[(11Z)-octadec-11-enoylamino]-4-O-phosphono-beta-D-glucopyranosyl}-2-[(3-oxotetradecanoyl)amino]-1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.77 | 0.81 | 42 | E55 |
| 2 | 697 | 0.76 | 0.80 | 45 | E55 |
| 3 | 584 | 0.65 | 0.76 | 64 | empty |
| 4 | 593 | 0.64 | 0.75 | 72 | empty |
| 5 | 307 | 0.52 | 0.74 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–C · 659 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 647 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 55 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2Z65 · Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y6Y9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9Y6Y9) · a predicted model of the same protein · chain C against A, TM-score 0.96
- 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 0.89
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 Q4G1L2
- Every structure of UniProt Q9Y6Y9
- Elsewhere: RCSB PDB 2Z65 · PDBe 2Z65 · UniProt O00206 · UniProt Q4G1L2 · UniProt Q9Y6Y9
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