MolNFT v1 · #55364 · protein

Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus

2YI8 · RNA-directed RNA polymerase: “Structure of the RNA polymerase VP1 from infectious pancreatic necrosis virus”. X-ray diffraction, 2 ligands (K, CL), 20 pockets (best druggability 0.76). MolNFT v1 #55364 on GenesisL1: 3D structure…

PDB: 2YI8
Type: protein
Length: 3,855 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase
EC: 2.7.7.48, 2.7.7.49
UniProt: P22173
Ligands: K, CL
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	RNA-directed RNA polymerase (EC 2.7.7.48, 2.7.7.49)	protein	771	46% helix, 14% strand	P22173

Ligands and binding sites

K · Potassium ion · metal · 5 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	878	0.76	0.79	116	empty
2	583	0.71	0.79	57	empty
3	331	0.71	0.84	43	empty
4	1005	0.70	0.75	109	CL
5	912	0.70	0.75	102	CL

Interfaces

7 interfaces between chains.

A–E · 1062 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1061 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1059 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 1058 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 422 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2YI8 · Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis 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
Every structure of UniProt P22173
Elsewhere: RCSB PDB 2YI8 · PDBe 2YI8 · UniProt P22173

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