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Zika NS5 polymerase domain

Analyse Zika NS5 polymerase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LD2
Type: protein
Length: 565 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.4
Source: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Molecule: RNA-directed RNA polymerase NS5
EC: 2.1.1.56, 2.1.1.57, 2.7.7.48
UniProt: A0A024B7W1
Ligands: KY3, ZN
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · resolution 1.4 · 1 distinct chain · 48% helix, 10% 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	565	48% helix, 10% strand	A0A024B7W1

Ligands and binding sites

KY3 · (1S,2S,4S,5R)-2,4-dimethoxy-5-thiophen-2-yl-cyclohexane-1-carboxylic 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

7 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	945	0.71	0.76	65	KY3
2	63	0.49	0.85	28	empty
3	63	0.36	0.78	17	empty
4	86	0.33	0.74	15	empty
5	68	0.28	0.73	17	empty

Compared structures

6LD2 · 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 6LD2 · PDBe 6LD2 · UniProt A0A024B7W1

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