Research workbench

Crystal structure of formaldehyde treated empty human enterovirus 71 particle (cryo at 100K)

Analyse Crystal structure of formaldehyde treated empty human enterovirus 71 particle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VBO
Type: protein
Length: 694 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein, capsid protein VP1; Genome polyprotein, capsid protein VP2; Genome…
UniProt: B2ZUN0
Ligands: NA
Pockets: 7 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein, capsid protein VP1	protein	218	9% helix, 34% strand	B2ZUN0
B	Genome polyprotein, capsid protein VP2	protein	237	13% helix, 38% strand	B2ZUN0
C	Genome polyprotein, capsid protein VP3	protein	239	12% helix, 33% strand	B2ZUN0

Ligands and binding sites

NA · Sodium ion · metal · chains A, C

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

Pockets

7 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	288	0.66	0.82	32	empty
2	240	0.52	0.76	36	empty
3	97	0.41	0.77	20	empty
4	79	0.41	0.79	16	empty
5	68	0.37	0.78	17	empty

Interfaces

3 interfaces between chains.

A–C · 3080 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 1812 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 1563 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3VBO · Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (cryo at… · 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 B2ZUN0
Elsewhere: RCSB PDB 3VBO · PDBe 3VBO · UniProt B2ZUN0

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