Research workbench

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 15

Analyse Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HMY
Type: protein
Length: 591 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase NS5
EC: 2.7.7.48
UniProt: Q6DLV0
Ligands: LNY, ZN
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase NS5 (EC 2.7.7.48)	protein	591	51% helix, 9% strand	Q6DLV0

Ligands and binding sites

LNY · 2,2'-(5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-1,3-phenylene)diacetic acid · ligand · chains A
ZN · Zinc 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.73	0.76	87	LNY
2	210	0.55	0.78	34	empty
3	61	0.29	0.74	17	empty
4	54	0.25	0.73	15	empty

Compared structures

5HMY · Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 15 · 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 Q6DLV0
Elsewhere: RCSB PDB 5HMY · PDBe 5HMY · UniProt Q6DLV0

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