SMTL ID : 7n8k.1 (1 other biounit)

LINE-1 endonuclease domain complex with Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.16, E.43 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.43, H2O.2, H2O.2, H2O.3

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: G.17, L.18, N.19, H.45 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.19, A:H.45 Hydrogen bonds: A:N.19 Salt bridges: A:H.45 ACT.4: 7 residues within 4Å: Chain A: T.192, T.224, N.225, S.228, D.229, H.230, S.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 ACT.5: 2 residues within 4Å: Chain A: H.7, K.218 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.7, A:K.218

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: A.21, R.24, H.25 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.24, A:H.25 SO4.6: 3 residues within 4Å: Chain A: K.88, R.134 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.88, A:R.134 SO4.7: 4 residues within 4Å: Chain A: K.88, K.90, R.134 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.88, A:K.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, I. et al., Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Nucleic Acids Res. (2021)

Release Date

2021-10-13

Peptides

LINE-1 retrotransposable element ORF2 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LINE-1 retrotransposable element ORF2 protein

Related Entries With Identical Sequence