Research workbench

Norwalk P domain a-trisaccharide complex

Analyse Norwalk P domain a-trisaccharide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D26
Type: protein
Length: 568 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 58 kd capsid protein
UniProt: Q83884
Ligands: GAL, FUC, NGA
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	58 kd capsid protein	protein	284	8% helix, 32% strand	Q83884
B	58 kd capsid protein	protein	284	9% helix, 32% strand	Q83884

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B

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

Pockets

3 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	514	0.77	0.84	83	empty
2	80	0.32	0.74	22	empty
3	55	0.28	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 1695 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3D26 · Norwalk P domain A-trisaccharide complex · 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 Q83884
Elsewhere: RCSB PDB 3D26 · PDBe 3D26 · UniProt Q83884

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