MolNFT v1 · #122242 · protein
The ligand-free structure of the mouse TLR4/MD-2 complex
5IJB · Toll-like receptor 4, variable lymphocyte receptor B chimera: “The ligand-free structure of the mouse TLR4/MD-2 complex”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.79). MolNFT v1 #122242 on GenesisL1: 3D…
- PDB
- 5IJB
- Type
- protein
- Length
- 1,455 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
- NAG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 4, variable lymphocyte receptor B chimera | protein | 593 | 10% helix, 21% strand | Q9QUK6, Q4G1L2 |
| C | Lymphocyte antigen 96 | protein | 136 | 3% helix, 54% strand | Q9JHF9 |
| B | Toll-like receptor 4, variable lymphocyte receptor B chimera | protein | 592 | 7% helix, 21% strand | Q9QUK6, Q4G1L2 |
| D | Lymphocyte antigen 96 | protein | 134 | 3% helix, 46% strand | Q9JHF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.79 | 0.93 | 24 | empty |
| 2 | 831 | 0.77 | 0.80 | 65 | empty |
| 3 | 1034 | 0.77 | 0.79 | 86 | empty |
| 4 | 562 | 0.71 | 0.80 | 60 | empty |
| 5 | 584 | 0.71 | 0.79 | 69 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1173 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1136 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 244 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 227 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5IJB · The ligand-free structure of the mouse TLR4/MD-2 complex · the same entry in another collection · chain D against D, 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 0.98
- Q9JHF9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9JHF9) · a predicted model of the same protein · chain D 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 Q9QUK6
- Every structure of UniProt Q4G1L2
- Every structure of UniProt Q9JHF9
- Elsewhere: RCSB PDB 5IJB · PDBe 5IJB · UniProt Q9QUK6 · UniProt Q4G1L2 · UniProt Q9JHF9
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