Research workbench
Crystal structure of a complex between bacillus subtilis flagellin and zebrafish toll-like receptor 5
Analyse Crystal structure of a complex between bacillus subtilis flagellin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GY2
- Type
- protein
- Length
- 1,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TLR5B PROTEIN,VARIABLE lymphocyte receptor B; Flagellin
- UniProt
- B3DIN1, Q4G1L2, E0U497
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TLR5B PROTEIN,VARIABLE lymphocyte receptor B | protein | 442 | 10% helix, 18% strand | B3DIN1, Q4G1L2 |
| C, D | Flagellin | protein | 169 | 63% helix, 7% strand | E0U497 |
| B | TLR5B PROTEIN,VARIABLE lymphocyte receptor B | protein | 441 | 10% helix, 18% strand | B3DIN1, Q4G1L2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.68 | 0.76 | 92 | empty |
| 2 | 545 | 0.66 | 0.77 | 68 | empty |
| 3 | 52 | 0.59 | 0.92 | 18 | empty |
| 4 | 407 | 0.58 | 0.75 | 41 | empty |
| 5 | 50 | 0.54 | 0.90 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1363 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1349 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5GY2 · Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish… · 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 B3DIN1
- Every structure of UniProt Q4G1L2
- Every structure of UniProt E0U497
- Elsewhere: RCSB PDB 5GY2 · PDBe 5GY2 · UniProt B3DIN1 · UniProt Q4G1L2 · UniProt E0U497
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