MolNFT v1 · #152993 · protein

The RNA-dependent RNA polymerase domain of dengue 3 NS5, bound with rk-0404678

6IZZ · Genome polyprotein: “The RNA-dependent RNA polymerase domain of dengue 3 NS5, bound with rk-0404678”. X-ray diffraction, 2 ligands (B5C, ZN), 5 pockets (best druggability 0.51). MolNFT v1 #152993 on GenesisL1: 3D structure, binding…

PDB: 6IZZ
Type: protein
Length: 568 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
UniProt: Q5I3C1
Ligands: B5C, ZN
Pockets: 5 · best druggability 0.51

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein	protein	568	49% helix, 10% strand	Q5I3C1

Ligands and binding sites

B5C · 2-oxo-2H-1,3-benzoxathiol-5-yl acetate · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.51	0.78	32	B5C
2	172	0.46	0.76	18	empty
3	138	0.43	0.75	24	empty
4	100	0.36	0.74	19	empty
5	52	0.30	0.76	14	empty

Compared structures

6IZZ · The RNA-dependent RNA polymerase domain of dengue 3 NS5, bound with RK-0404678 · 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 Q5I3C1
Elsewhere: RCSB PDB 6IZZ · PDBe 6IZZ · UniProt Q5I3C1

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