Research workbench

Bel beta-trefoil complex with N-acetylgalactosamine

Analyse Bel beta-trefoil complex with N-acetylgalactosamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4I4V
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bel beta-trefoil
Ligands: NGA
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Bel beta-trefoil	protein	146	8% helix, 38% strand	—

Ligands and binding sites

NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 6 copies · chains A, D, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.80	0.81	141	TRS
2	77	0.37	0.77	20	NGA

Interfaces

4 interfaces between chains.

C–D · 870 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 799 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 329 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 275 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4I4V · BEL beta-trefoil complex with N-acetylgalactosamine · 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
Elsewhere: RCSB PDB 4I4V · PDBe 4I4V

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