Research workbench
Crystal structure of mouse TLR4/MD-2 in complex with sulfatides
Analyse Crystal structure of mouse TLR4/MD-2 in complex with sulfatides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MLM
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 4,VARIABLE lymphocyte receptor B; Lymphocyte antigen 96
- EC
- 3.2.2.6
- UniProt
- Q9QUK6, Q4G1L2, Q9JHF9
- Ligands
- ZKM, NAG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 4,VARIABLE lymphocyte receptor B (EC 3.2.2.6) | protein | 590 | 10% helix, 22% strand | Q9QUK6, Q4G1L2 |
| C | Lymphocyte antigen 96 | protein | 136 | 3% helix, 56% strand | Q9JHF9 |
Ligands and binding sites
- ZKM · N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide · ligand · 3 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.77 | 0.81 | 42 | ZKM |
| 2 | 508 | 0.69 | 0.79 | 49 | empty |
| 3 | 123 | 0.46 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–C · 1153 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7MLM · Crystal structure of mouse TLR4/MD-2 in complex with sulfatides · 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 7MLM · PDBe 7MLM · UniProt Q9QUK6 · UniProt Q4G1L2 · UniProt Q9JHF9
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