Research workbench

Crystal structure of the biglycan dimer core protein

Analyse Crystal structure of the biglycan dimer core protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FT3
Type: protein
Length: 1,821 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biglycan
UniProt: P21809
Ligands: NAG
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Biglycan	protein	303	8% helix, 15% strand	P21809
D	Biglycan	protein	304	8% helix, 16% strand	P21809
F	Biglycan	protein	305	8% helix, 15% strand	P21809

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
FLC · Citrate anion · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	382	0.77	0.87	55	empty
2	391	0.76	0.86	62	empty
3	508	0.75	0.83	76	empty
4	544	0.64	0.76	57	FLC
5	444	0.63	0.77	41	FLC

Interfaces

5 interfaces between chains.

E–F · 1417 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1409 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1404 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 321 Å² buried · 1 hydrogen bond · protein-protein
A–F · 108 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 6 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).

Compared structures

2FT3 · Crystal structure of the biglycan dimer core protein · the same entry in another collection · chain F against F, TM-score 1.00
P21809 · AlphaFold monomer V2.0 prediction for biglycan (P21809) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P21809
Elsewhere: RCSB PDB 2FT3 · PDBe 2FT3 · UniProt P21809

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