SMTL ID : 6ozf.2 (1 other biounit)

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 3 residues within 4Å: Chain A: D.43, H.214 Chain B: G.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, A:H.214, H2O.1, H2O.5, H2O.7 CA.7: 2 residues within 4Å: Chain B: T.3, G.7 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: E.72, K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.99, A:K.99 GOL.3: 2 residues within 4Å: Chain A: K.222, F.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.222

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: W.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.156 Water bridges: A:W.156

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 7 residues within 4Å: Chain A: E.68, V.69, V.70, S.71, K.99, R.101, L.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.71, A:K.99 Water bridges: A:V.69, A:S.71

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: D.43, L.44, N.110 Chain B: A.6, G.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.44, A:L.44, A:N.110

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endonuclease V

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