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Crystal structure of zikv NS3 helicase in complex with ADP and MN2+

Analyse Crystal structure of zikv NS3 helicase in complex with ADP and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K8U
Type: protein
Length: 442 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zika virus NS3 helicase
Ligands: ADP, MN, CL
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Zika virus NS3 helicase	protein	442	33% helix, 18% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1108	0.84	0.85	89	CL
2	224	0.56	0.79	43	ADP, MN
3	141	0.46	0.77	31	empty
4	53	0.36	0.80	13	empty

Compared structures

5K8U · Crystal structure of ZIKV NS3 helicase in complex with ADP and Mn2+ · 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
Elsewhere: RCSB PDB 5K8U · PDBe 5K8U

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