MolNFT v1 · #118508 · protein

Dengue serotype 3 RNA-dependent RNA polymerase bound to fd-83-KI26

5F41 · Genome polyprotein: “Dengue serotype 3 RNA-dependent RNA polymerase bound to fd-83-KI26”. X-ray diffraction, 2 ligands (5V6, ZN), 6 pockets (best druggability 0.69). MolNFT v1 #118508 on GenesisL1: 3D structure, binding sites and…

PDB: 5F41
Type: protein
Length: 585 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
UniProt: Q6DLV0
Ligands: 5V6, ZN
Pockets: 6 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein	protein	585	51% helix, 10% strand	Q6DLV0

Ligands and binding sites

5V6 · 2-(4-methoxy-3-thiophen-3-yl-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

6 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	747	0.69	0.76	68	5V6
2	113	0.49	0.80	20	empty
3	65	0.46	0.83	19	empty
4	97	0.43	0.78	22	empty
5	60	0.27	0.73	16	empty

Compared structures

5F41 · Dengue serotype 3 RNA-dependent RNA polymerase bound to fd-83-KI26 · 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 5F41 · PDBe 5F41 · UniProt Q6DLV0

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