SMTL ID : 6ozr.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: D.52, D.126, D.240 Chain C: U.12 Ligands: K.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.126, A:D.240, H2O.1, H2O.2 MG.10: 5 residues within 4Å: Chain B: D.52, D.126, D.240 Chain D: U.12 Ligands: K.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.126, B:D.240, H2O.5, H2O.10 MG.16: 1 residues within 4Å: Chain C: U.18 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain D: U.18 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.52, V.53, D.126 Chain C: A.11, U.12 Ligands: MG.1 No protein-ligand interaction detected (PLIP) K.11: 6 residues within 4Å: Chain B: D.52, V.53, D.126 Chain D: A.11, U.12 Ligands: MG.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, H2O.6

3 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 7 residues within 4Å: Chain A: F.42, S.43, G.44, L.45, Q.46, Y.72, P.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.42, A:G.44, A:L.45, A:Q.46 TLA.4: 4 residues within 4Å: Chain A: D.32, T.33, E.34, R.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.34 Water bridges: A:R.31 TLA.12: 8 residues within 4Å: Chain B: S.41, F.42, S.43, G.44, L.45, Q.46, Y.72, P.73 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.44, B:L.45, B:Q.46, B:Y.72

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.46, K.47, Q.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.47, A:K.47 Water bridges: A:Q.121 GOL.6: 5 residues within 4Å: Chain A: L.168, L.175, T.182, F.183, P.184 No protein-ligand interaction detected (PLIP)

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

PGE.7: 6 residues within 4Å: Chain A: P.73, L.75, H.225, H.226, C.228, R.229 No protein-ligand interaction detected (PLIP) PGE.13: 6 residues within 4Å: Chain B: P.73, L.75, H.225, H.226, C.228, R.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.229, B:R.229

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

EDO.8: 3 residues within 4Å: Chain A: M.195, E.218, R.222 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.218, A:R.222 EDO.9: 3 residues within 4Å: Chain A: S.71, K.76, V.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.71 EDO.14: 3 residues within 4Å: Chain B: Y.79, E.80, K.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.80, B:K.114 Water bridges: B:E.115 EDO.15: 2 residues within 4Å: Chain B: F.98, P.102 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.20, B:E.20

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endonuclease V

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