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Crystal structure of coxsackie virus B3 3D polymerase in complex with gpc-N114 inhibitor

Analyse Crystal structure of coxsackie virus B3 3D polymerase in complex with gpc-N114… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y2A
Type: protein
Length: 466 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3D polymerase
UniProt: P03313
Ligands: 1FS, SO4
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3D polymerase	protein	466	42% helix, 15% strand	P03313

Ligands and binding sites

1FS · 2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile) · ligand · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A
GOL · Glycerol · additive · 4 copies · chains A

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

Pockets

5 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	463	0.67	0.79	58	SO4, GOL
2	236	0.56	0.78	32	1FS
3	83	0.42	0.79	22	empty
4	100	0.40	0.76	17	SO4
5	50	0.26	0.74	11	empty

Compared structures

4Y2A · Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03313
Elsewhere: RCSB PDB 4Y2A · PDBe 4Y2A · UniProt P03313

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