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Dengue serotype 3 RNA-dependent RNA polymerase bound to nitd-107

Analyse Dengue serotype 3 RNA-dependent RNA polymerase bound to nitd-107 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VWS
Type: protein
Length: 592 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-structural protein 5
EC: 2.7.7.48
UniProt: Q6DLV0
Ligands: VWS, ZN
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-structural protein 5 (EC 2.7.7.48)	protein	592	49% helix, 10% strand	Q6DLV0

Ligands and binding sites

VWS · 5-{[(4-chlorophenyl)sulfonyl]amino}-2-methyl-1-benzofuran-3-carboxylic acid · ligand · 2 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

3 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	1166	0.74	0.77	96	VWS
2	195	0.67	0.86	43	empty
3	73	0.48	0.83	19	empty

Compared structures

3VWS · Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-107 · 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 3VWS · PDBe 3VWS · UniProt Q6DLV0

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