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Crystal structure of human enterovirus 71

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

PDB: 3VBS
Type: protein
Length: 842 residues
Chains: 4
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, B2ZUN1
Ligands: SPH
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein, capsid protein VP1	protein	297	14% helix, 27% strand	B2ZUN0
B	Genome polyprotein, capsid protein VP2	protein	245	13% helix, 38% strand	B2ZUN1
C	Genome polyprotein, capsid protein VP3	protein	242	13% helix, 30% strand	B2ZUN0
D	Genome polyprotein, capsid protein VP4	protein	58	12% helix, 12% strand	B2ZUN0

Ligands and binding sites

SPH · Sphingosine · ligand · chains A

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

Pockets

13 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	428	0.78	0.86	58	SPH
2	257	0.59	0.80	38	empty
3	197	0.50	0.76	29	empty
4	135	0.49	0.79	25	empty
5	119	0.48	0.79	23	empty

Interfaces

6 interfaces between chains.

A–C · 4028 Å² buried · 60 hydrogen bonds · protein-protein
A–B · 2700 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 1661 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1525 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1138 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3VBS · Crystal structure of human Enterovirus 71 · 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
Every structure of UniProt B2ZUN1
Elsewhere: RCSB PDB 3VBS · PDBe 3VBS · UniProt B2ZUN0 · UniProt B2ZUN1

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