MolNFT v1 · #121155 · protein

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 5

5HMW · RNA-directed RNA polymerase NS5: “Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 5”. X-ray diffraction, 2 ligands (LNW, ZN), 5 pockets (best druggability 0.70). MolNFT v1 #121155 on GenesisL1: 3D structure, binding…

PDB: 5HMW
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: LNW, ZN
Pockets: 5 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase NS5 (EC 2.7.7.48)	protein	591	51% helix, 10% strand	Q6DLV0

Ligands and binding sites

LNW · 2,2'-biphenyl-3,5-diyldiacetic acid · ligand · 2 copies · 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	805	0.70	0.76	65	LNW
2	55	0.50	0.87	17	empty
3	101	0.46	0.79	21	empty
4	84	0.41	0.78	21	empty
5	97	0.39	0.76	20	LNW

Compared structures

5HMW · Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 5 · 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 5HMW · PDBe 5HMW · UniProt Q6DLV0

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