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Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E. COLI: the wt enzyme at 2.8 resolution.

Analyse Crystal structure of the DNA repair enzyme endonuclease-VIII (nei) from E.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q39
Type: protein
Length: 257 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease VIII
EC: 3.2.2.-
UniProt: P50465
Ligands: CA, ZN
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endonuclease VIII (EC 3.2.2.-)	protein	257	28% helix, 22% strand	P50465

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.47	0.76	27	empty
2	175	0.45	0.75	40	empty

Compared structures

1Q39 · Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT… · the same entry in another collection · chain A against A, TM-score 1.00
P50465 · AlphaFold monomer V2.0 prediction for endonuclease 8 (P50465) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 P50465
Elsewhere: RCSB PDB 1Q39 · PDBe 1Q39 · UniProt P50465

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