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Mopeia virus exonuclease domain complexed with manganese

Analyse Mopeia virus exonuclease domain complexed with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SX8
Type: protein
Length: 397 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
EC: 3.1.13.-
UniProt: Q5S581
Ligands: ZN, MN
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein (EC 3.1.13.-)	protein	198	38% helix, 16% strand	Q5S581
B	Nucleoprotein (EC 3.1.13.-)	protein	199	38% helix, 17% strand	Q5S581

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B

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	205	0.56	0.79	39	empty
2	217	0.47	0.74	25	MN
3	170	0.47	0.76	19	MN
4	88	0.44	0.79	15	empty
5	80	0.38	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 343 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6SX8 · Mopeia Virus Exonuclease domain complexed with Manganese · 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 Q5S581
Elsewhere: RCSB PDB 6SX8 · PDBe 6SX8 · UniProt Q5S581

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