MolNFT v2 · #220364 · protein + RNA

Structure of LINE-1 ORF2p with an oligo(A) template

8SXU · LINE-1 retrotransposable element ORF2 protein: “Structure of LINE-1 ORF2p with an oligo(A) template”. Electron microscopy at 3.66, 16 pockets (best druggability 0.77). MolNFT v2 #220364 on GenesisL1: 3D structure, binding sites and…

PDB: 8SXU
Type: protein + RNA
Length: 736 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.66
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: LINE-1 retrotransposable element ORF2 protein; RNA (25-mer)
EC: 2.7.7.49, 3.1.21.-
UniProt: O00370
Pockets: 16 · best druggability 0.77

Structure

electron microscopy · resolution 3.66 · 2 distinct chains · 49% helix, 10% 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	726	49% helix, 10% strand	O00370
C	RNA (25-mer)	rna	10	—	—

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.77	0.95	27	empty
2	72	0.75	0.98	21	empty
3	93	0.74	0.95	28	empty
4	531	0.70	0.80	46	empty
5	101	0.61	0.87	27	empty

Interfaces

1 interface between chains.

A–C · 1071 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

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 0.98

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 8SXU · PDBe 8SXU · UniProt O00370

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