GL1X · GenesisL1 explorer

MolNFT v1 · #182923 · protein + DNA

Line-1 endonuclease domain complex with DNA

7N8S · Line-1 retrotransposable element ORF2 protein: “Line-1 endonuclease domain complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #182923 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7N8S
Type
protein + DNA
Length
262 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Line-1 retrotransposable element ORF2 protein; DNA…
EC
2.7.7.49, 3.1.21.-
UniProt
O00370
Pockets
5 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 34% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALine-1 retrotransposable element ORF2 protein (EC 2.7.7.49, 3.1.21.-)protein23224% helix, 34% strandO00370
DDNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)- 3')dna15——
CDNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)- 3')dna15——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11300.660.8921empty
22310.500.7522empty
3670.390.7912empty
4910.310.7317empty
5770.300.7316empty

Interfaces

3 interfaces between chains.

  • D–C · 646 Ų buried · 45 hydrogen bonds · nucleic-nucleic
  • A–C · 529 Ų buried · 15 hydrogen bonds · protein-nucleic
  • A–D · 333 Ų buried · 5 hydrogen bonds · protein-nucleic

Compared structures

  • 7N8S · LINE-1 endonuclease domain complex with DNA · 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

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