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Active state of the nuclease

Analyse Active state of the nuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZO5
Type: protein
Length: 411 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative 3'-5' exonuclease family protein
EC: 3.1.13.-
UniProt: A0A1S7QSB2
Ligands: MN, SO4
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative 3'-5' exonuclease family protein (EC 3.1.13.-)	protein	205	44% helix, 15% strand	A0A1S7QSB2
B	Putative 3'-5' exonuclease family protein (EC 3.1.13.-)	protein	206	41% helix, 15% strand	A0A1S7QSB2

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	359	0.63	0.78	44	MN, SO4
2	209	0.57	0.80	26	MN, SO4
3	99	0.41	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 1341 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5ZO5 · active state of the nuclease · 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 A0A1S7QSB2
Elsewhere: RCSB PDB 5ZO5 · PDBe 5ZO5 · UniProt A0A1S7QSB2

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