Research workbench
Crystal structure of N-terminal fragment of zebrafish toll-like receptor 5 (TLR5) with lamprey variable lymphocyte receptor 2 (VLR2) bound
Analyse Crystal structure of N-terminal fragment of zebrafish toll-like receptor 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXA
- Type
- protein
- Length
- 1,268 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 5B, variable lymphocyte receptor B chimera; Variable lymphocyte…
- UniProt
- F8W3J5, Q4G1L2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 5B, variable lymphocyte receptor B chimera | protein | 443 | 10% helix, 18% strand | F8W3J5, Q4G1L2 |
| B | Toll-like receptor 5B, variable lymphocyte receptor B chimera | protein | 441 | 9% helix, 18% strand | F8W3J5, Q4G1L2 |
| C, D | Variable lymphocyte receptor 2 | protein | 192 | 13% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.73 | 0.78 | 78 | EDO |
| 2 | 227 | 0.54 | 0.78 | 39 | empty |
| 3 | 218 | 0.51 | 0.76 | 36 | empty |
| 4 | 108 | 0.44 | 0.78 | 19 | empty |
| 5 | 94 | 0.44 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1012 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 966 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6BXA · Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with… · the same entry in another collection · chain A against A, 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 F8W3J5
- Every structure of UniProt Q4G1L2
- Elsewhere: RCSB PDB 6BXA · PDBe 6BXA · UniProt F8W3J5 · UniProt Q4G1L2
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