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Crystal structure of EV71 3DPOL-vpg

Analyse Crystal structure of EV71 3DPOL-vpg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IKA
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3DPOL; Vpg
UniProt: I3UIB4, Q0ZSY4
Ligands: NI
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3DPOL	protein	462	41% helix, 16% strand	I3UIB4
D	Vpg	protein	20	0% helix, 10% strand	Q0ZSY4

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	486	0.60	0.75	48	empty
2	301	0.56	0.76	32	empty
3	202	0.53	0.78	23	empty
4	160	0.41	0.73	25	empty

Interfaces

1 interface between chains.

A–D · 724 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4IKA · Crystal structure of EV71 3Dpol-VPg · 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 I3UIB4
Every structure of UniProt Q0ZSY4
Elsewhere: RCSB PDB 4IKA · PDBe 4IKA · UniProt I3UIB4 · UniProt Q0ZSY4

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