Research workbench
Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61
Analyse Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z66
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor B, toll-like receptor 4
- UniProt
- Q4G1L2, O00206
- Ligands
- NAG, BMA, FUL, SO4
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Variable lymphocyte receptor B, toll-like receptor 4 | protein | 306 | 11% helix, 24% strand | Q4G1L2, O00206 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 8 copies
- FUL · beta-L-fucopyranose · sugar · 4 copies
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.69 | 0.81 | 58 | SO4 |
| 2 | 363 | 0.67 | 0.81 | 52 | SO4 |
| 3 | 52 | 0.51 | 0.87 | 12 | empty |
| 4 | 50 | 0.48 | 0.86 | 14 | empty |
| 5 | 51 | 0.48 | 0.85 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 560 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 433 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 2Z66 · Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 · 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 0.93
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 Q4G1L2
- Every structure of UniProt O00206
- Elsewhere: RCSB PDB 2Z66 · PDBe 2Z66 · UniProt Q4G1L2 · UniProt O00206
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