SMTL ID : 6ozi.1

Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.1: 2 residues within 4Å: Chain A: N.71, T.72 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.72, H2O.7 K.4: 3 residues within 4Å: Chain C: I.5 Chain D: T.17 Ligands: K.6 No protein-ligand interaction detected (PLIP) K.5: 2 residues within 4Å: Chain C: T.9, G.10 No protein-ligand interaction detected (PLIP) K.6: 4 residues within 4Å: Chain C: T.7 Chain D: T.16, T.17 Ligands: K.4 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: K.34, K.36, Y.37, N.107, L.108, E.109, Q.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.106, A:Q.111 PGE.3: 4 residues within 4Å: Chain B: K.34, K.36, Q.111, R.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.139, B:R.139 Water bridges: B:K.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, J. et al., Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol.Cell (2019)

Release Date

2019-09-04

Peptides

endonuclease V isoform X2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

endonuclease V isoform X2