Research workbench

Atomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry

Analyse Atomic structure of a non-enveloped virus reveals pH sensors for a coordinated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J9D
Type: protein
Length: 746 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP2
UniProt: B7U676
Ligands: ZN
Pockets: 7 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 28% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer capsid protein VP2	protein	746	28% helix, 18% strand	B7U676

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.75	0.85	36	empty
2	201	0.61	0.83	29	empty
3	378	0.58	0.75	35	empty
4	91	0.37	0.76	16	empty
5	89	0.35	0.74	17	empty

Compared structures

3J9D · Atomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of… · 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 B7U676
Elsewhere: RCSB PDB 3J9D · PDBe 3J9D · UniProt B7U676

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