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Inactive state of the nuclease

Analyse Inactive 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: 5ZO4
Type: protein
Length: 413 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: 2 · best druggability 0.67

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	207	43% helix, 14% strand	A0A1S7QSB2
B	Putative 3'-5' exonuclease family protein (EC 3.1.13.-)	protein	206	42% helix, 15% strand	A0A1S7QSB2

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

2 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	538	0.67	0.77	49	SO4, MN
2	513	0.64	0.76	48	SO4, MN

Interfaces

1 interface between chains.

A–B · 1343 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5ZO4 · inactive 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 5ZO4 · PDBe 5ZO4 · UniProt A0A1S7QSB2

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