Research workbench
Cryo-EM of aedes aegypti TOLL5A trimer bound to SPZ1C
Analyse Cryo-EM of aedes aegypti TOLL5A trimer bound to SPZ1C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B1C
- Type
- protein
- Length
- 2,440 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor; AAEL013433-pa
- UniProt
- A0A6I8TEX2, Q16J57
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 10% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Toll-like receptor | protein | 750 | 11% helix, 15% strand | A0A6I8TEX2 |
| A | Toll-like receptor | protein | 752 | 11% helix, 18% strand | A0A6I8TEX2 |
| D | AAEL013433-pa | protein | 96 | 4% helix, 43% strand | Q16J57 |
| P | AAEL013433-pa | protein | 91 | 3% helix, 41% strand | Q16J57 |
| B | Toll-like receptor | protein | 751 | 11% helix, 17% strand | A0A6I8TEX2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains C, A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.86 | 0.87 | 138 | empty |
| 2 | 631 | 0.84 | 0.89 | 83 | empty |
| 3 | 325 | 0.83 | 0.92 | 71 | empty |
| 4 | 958 | 0.81 | 0.83 | 100 | empty |
| 5 | 185 | 0.80 | 0.95 | 31 | empty |
Interfaces
7 interfaces between chains.
- D–B · 1402 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 1098 Ų buried · 12 hydrogen bonds · protein-protein
- D–P · 1016 Ų buried · 12 hydrogen bonds · protein-protein
- A–P · 519 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 7B1C · Cryo-EM of Aedes Aegypti Toll5A trimer bound to Spz1C · the same entry in another collection · chain C against C, TM-score 1.00
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 A0A6I8TEX2
- Every structure of UniProt Q16J57
- Elsewhere: RCSB PDB 7B1C · PDBe 7B1C · UniProt A0A6I8TEX2 · UniProt Q16J57
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