MolNFT v1 · #85943 · protein

Crystal structure of the N-terminal domain of drosophila toll receptor

4ARN · Toll receptor, variable lymphocyte receptor B.61 chimera: “Crystal structure of the N-terminal domain of drosophila toll receptor”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 11 pockets (best druggability 0.82). MolNFT v1 #85943…

PDB: 4ARN
Type: protein
Length: 1,095 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll receptor, variable lymphocyte receptor B.61 chimera
UniProt: P08953, Q4G1L2
Ligands: NAG, FUC, BMA, MAN
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll receptor, variable lymphocyte receptor B.61 chimera	protein	277	14% helix, 22% strand	P08953, Q4G1L2
B, C	Toll receptor, variable lymphocyte receptor B.61 chimera	protein	273	14% helix, 23% strand	P08953, Q4G1L2
D	Toll receptor, variable lymphocyte receptor B.61 chimera	protein	272	13% helix, 23% strand	P08953, Q4G1L2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B, D
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
MAN · alpha-D-mannopyranose · sugar
MLI · Malonate ion · additive · 2 copies · chains A, B, C

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	1131	0.82	0.83	104	MLI
2	841	0.81	0.84	80	empty
3	96	0.75	0.97	18	MLI
4	185	0.59	0.82	39	empty
5	145	0.47	0.78	27	empty

Interfaces

5 interfaces between chains.

A–B · 1128 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 697 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 663 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 557 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 554 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

4ARN · Crystal structure of the N-terminal domain of Drosophila Toll receptor · the same entry in another collection · chain A against A, TM-score 1.00
P08953 · AlphaFold monomer V2.0 prediction for protein toll (P08953) · a predicted model of the same protein · chain D against A, TM-score 0.89

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 P08953
Every structure of UniProt Q4G1L2
Elsewhere: RCSB PDB 4ARN · PDBe 4ARN · UniProt P08953 · UniProt Q4G1L2

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