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The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with rk-0404678

Analyse The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with rk-0404678 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IZX
Type: protein
Length: 581 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
UniProt: C6L435
Ligands: B5C, CO, ZN
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein	protein	581	47% helix, 11% strand	C6L435

Ligands and binding sites

B5C · 2-oxo-2H-1,3-benzoxathiol-5-yl acetate · ligand · 2 copies · chains A
CO · Cobalt (II) ion · metal · 9 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

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	550	0.64	0.75	65	CO, B5C
2	102	0.55	0.84	17	B5C
3	207	0.53	0.77	29	empty
4	129	0.47	0.78	21	empty
5	57	0.34	0.77	14	empty

Compared structures

6IZX · The RNA-dependent RNA polymerase domain of dengue 2 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 C6L435
Elsewhere: RCSB PDB 6IZX · PDBe 6IZX · UniProt C6L435

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