MolNFT v1 · #81828 · protein

Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with salmonella flagellin

3V47 · Toll-like receptor 5B and variable lymphocyte receptor B.61…: “Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with salmonella flagellin”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability…

PDB: 3V47
Type: protein
Length: 1,461 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 5B and variable lymphocyte receptor B.61 chimeric protein; Flagellin
UniProt: B3DIN1, Q4G1L2, Q06971
Ligands: NAG
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Toll-like receptor 5B and variable lymphocyte receptor B.61 chimeric protein	protein	441	10% helix, 19% strand	B3DIN1, Q4G1L2
C	Flagellin	protein	295	38% helix, 23% strand	Q06971
D	Flagellin	protein	284	41% helix, 22% strand	Q06971

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1130	0.78	0.80	93	empty
2	409	0.62	0.77	57	empty
3	113	0.62	0.87	26	empty
4	339	0.60	0.78	52	empty
5	216	0.44	0.73	31	empty

Interfaces

5 interfaces between chains.

B–D · 1783 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 1782 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 807 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 221 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 175 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

3V47 · Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
Q06971 · AlphaFold monomer V2.0 prediction for flagellin (Q06971) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 Q06971
Elsewhere: RCSB PDB 3V47 · PDBe 3V47 · UniProt B3DIN1 · UniProt Q4G1L2 · UniProt Q06971

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.