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Crystal structure of capsid P domain of norovirus GI.3 dsv complexed with GALA1-3GALB1-4GLC

Analyse Crystal structure of capsid P domain of norovirus GI.3 dsv complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EQT
Type: protein
Length: 602 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid P domain
Ligands: BGC, GAL, GLA
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid P domain	protein	304	9% helix, 32% strand	—
B	Capsid P domain	protein	298	9% helix, 31% strand	—

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · chains A
GAL · beta-D-galactopyranose · sugar · chains A
GLA · alpha-D-galactopyranose · sugar · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	539	0.83	0.89	77	empty
2	62	0.74	0.99	20	empty
3	119	0.35	0.73	29	empty
4	93	0.33	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 1579 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7EQT · Crystal structure of capsid P domain of norovirus GI.3 DSV complexed with… · the same entry in another collection · chain B against B, 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 7EQT · PDBe 7EQT

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