MolNFT v1 · #155612 · protein

Zika NS5 polymerase domain

6LD3 · RNA-directed RNA polymerase NS5: “Zika NS5 polymerase domain”. X-ray diffraction, 3 ligands (G8O, FB2, ZN), 4 pockets (best druggability 0.75). MolNFT v1 #155612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LD3
Type: protein
Length: 578 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase NS5
EC: 2.1.1.56, 2.1.1.57, 2.7.7.48
UniProt: A0A024B7W1
Ligands: G8O, FB2, ZN
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48)	protein	578	49% helix, 12% strand	A0A024B7W1

Ligands and binding sites

G8O · 2,4-dimethoxy-5-thiophen-2-yl-benzoic acid · ligand · chains A
FB2 · benzenesulfonamide · 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

4 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	925	0.75	0.78	73	G8O, FB2
2	98	0.43	0.78	23	empty
3	60	0.43	0.82	28	empty
4	71	0.32	0.75	15	empty

Compared structures

6LD3 · Zika NS5 polymerase domain · 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 A0A024B7W1
Elsewhere: RCSB PDB 6LD3 · PDBe 6LD3 · UniProt A0A024B7W1

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