MolNFT v1 · #104927 · protein

Crystal structure of empty hepatitis a virus

4QPG · Capsid protein VP1: “Crystal structure of empty hepatitis a virus”. X-ray diffraction, 2 ligands (CL, SO4), 5 pockets (best druggability 0.52). MolNFT v1 #104927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QPG
Type: protein
Length: 675 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP0; Capsid protein VP3
Ligands: CL, SO4
Pockets: 5 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	225	11% helix, 35% strand	—
B	Capsid protein VP0	protein	204	10% helix, 40% strand	—
C	Capsid protein VP3	protein	246	10% helix, 37% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	245	0.52	0.75	35	empty
2	84	0.37	0.77	24	empty
3	76	0.33	0.75	24	empty
4	67	0.33	0.76	11	empty
5	66	0.30	0.74	15	empty

Interfaces

3 interfaces between chains.

A–C · 3512 Å² buried · 73 hydrogen bonds · protein-protein
B–C · 1506 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1138 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4QPG · Crystal structure of empty hepatitis A virus · 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 4QPG · PDBe 4QPG

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