MolNFT v1 · #30939 · protein

Crystal structure of the rotavirus strain ds-1 VP8* core

2AEN · Outer capsid protein VP4, VP8* core: “Crystal structure of the rotavirus strain ds-1 VP8* core”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #30939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2AEN
Type: protein
Length: 1,312 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP4, VP8* core
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Outer capsid protein VP4, VP8* core	protein	164	8% helix, 56% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains B, A, D, E, H, G
EOH · Ethanol · additive · 4 copies · chains A, D, B, G, E, H

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	797	0.71	0.77	78	EOH, GOL
2	372	0.58	0.76	40	empty
3	324	0.57	0.76	38	empty
4	258	0.51	0.75	31	empty
5	146	0.48	0.77	24	empty

Interfaces

9 interfaces between chains.

E–F · 482 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 456 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 443 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 439 Å² buried · 11 hydrogen bonds · protein-protein
D–H · 419 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2AEN · Crystal structure of the rotavirus strain DS-1 VP8* core · 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
Elsewhere: RCSB PDB 2AEN · PDBe 2AEN

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