MolNFT v1 · #144558 · protein
Crystal structure of N-terminal fragment of zebrafish toll-like receptor 5 (TLR5) with lamprey variable lymphocyte receptor 9 (VLR9) bound
6BXC · Toll-like receptor 5B, variable lymphocyte receptor B…: “Crystal structure of N-terminal fragment of zebrafish toll-like receptor 5 (TLR5) with lamprey variable…”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability…
- PDB
- 6BXC
- Type
- protein
- Length
- 1,213 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
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 5B, variable lymphocyte receptor B chimera | protein | 441 | 10% helix, 18% strand | F8W3J5, Q4G1L2 |
| D | Variable lymphocyte receptor 9 (VLR9) | protein | 166 | 14% helix, 17% strand | — |
| C | Variable lymphocyte receptor 9 (VLR9) | protein | 165 | 13% helix, 16% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.74 | 0.80 | 59 | empty |
| 2 | 424 | 0.74 | 0.84 | 57 | empty |
| 3 | 51 | 0.65 | 0.94 | 17 | empty |
| 4 | 137 | 0.61 | 0.85 | 22 | empty |
| 5 | 173 | 0.53 | 0.79 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1193 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1176 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 908 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6BXC · 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 6BXC · PDBe 6BXC · UniProt F8W3J5 · UniProt Q4G1L2
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