Research workbench

X-ray structure of a native calicivirus

Analyse X-ray structure of a native calicivirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GH8
Type: protein
Length: 1,629 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: P36285
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Capsid protein	protein	544	10% helix, 36% strand	P36285
B	Capsid protein	protein	541	9% helix, 37% strand	P36285

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.71	0.87	52	empty
2	185	0.67	0.86	29	empty
3	120	0.67	0.90	27	empty
4	377	0.65	0.79	44	empty
5	62	0.63	0.93	17	empty

Interfaces

3 interfaces between chains.

A–C · 1674 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1272 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1097 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2GH8 · X-ray structure of a native calicivirus · 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 P36285
Elsewhere: RCSB PDB 2GH8 · PDBe 2GH8 · UniProt P36285

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