MolNFT v1 · #182916 · protein

Line-1 endonuclease domain complex with mg

7N8K · Line-1 retrotransposable element ORF2 protein: “Line-1 endonuclease domain complex with mg”. X-ray diffraction, 2 ligands (MG, SO4), 5 pockets (best druggability 0.57). MolNFT v1 #182916 on GenesisL1: 3D structure, binding sites and…

PDB: 7N8K
Type: protein
Length: 465 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Line-1 retrotransposable element ORF2 protein
EC: 2.7.7.49, 3.1.21.-
UniProt: O00370
Ligands: MG, SO4
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Line-1 retrotransposable element ORF2 protein (EC 2.7.7.49, 3.1.21.-)	protein	233	26% helix, 36% strand	O00370
B	Line-1 retrotransposable element ORF2 protein (EC 2.7.7.49, 3.1.21.-)	protein	232	26% helix, 36% strand	O00370

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains A, B

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

Pockets

5 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	115	0.57	0.85	25	ACT
2	167	0.49	0.78	25	empty
3	146	0.47	0.77	25	empty
4	113	0.35	0.73	22	empty
5	87	0.32	0.73	21	empty

Interfaces

1 interface between chains.

A–B · 1079 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7N8K · LINE-1 endonuclease domain complex with Mg · the same entry in another collection · chain A against A, TM-score 1.00
O00370 · AlphaFold monomer V2.0 prediction for line-1 retrotransposable element ORF2 protein… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O00370
Elsewhere: RCSB PDB 7N8K · PDBe 7N8K · UniProt O00370

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