Research workbench

Dengue serotype 3 RNA-dependent RNA polymerase bound to jf-31-MG46

Analyse Dengue serotype 3 RNA-dependent RNA polymerase bound to jf-31-MG46 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F3T
Type: protein
Length: 585 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase
UniProt: Q6DLV0
Ligands: 5UH, ZN
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-dependent RNA polymerase	protein	585	51% helix, 10% strand	Q6DLV0

Ligands and binding sites

5UH · 2-(4-methoxy-3-phenyl-phenyl)ethanoic 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

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	749	0.69	0.76	64	5UH
2	220	0.53	0.77	34	empty
3	52	0.45	0.84	15	empty
4	91	0.41	0.77	21	empty
5	56	0.26	0.73	15	empty

Compared structures

5F3T · Dengue serotype 3 RNA-dependent RNA polymerase bound to JF-31-MG46 · 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 5F3T · PDBe 5F3T · UniProt Q6DLV0

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