SMTL ID : 6ozk.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.47, D.235, R.239 Chain C: U.12 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.47, A:D.235, H2O.1, H2O.3, H2O.5 CA.2: 4 residues within 4Å: Chain A: D.47, D.121 Chain C: A.11, U.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, A:D.121, H2O.1, H2O.5 CA.11: 3 residues within 4Å: Chain B: D.47, D.235 Chain D: U.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.47, B:D.235, H2O.4, H2O.5, H2O.6 CA.12: 5 residues within 4Å: Chain B: D.47, V.48, D.121 Chain D: A.11, U.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.47, B:D.121, H2O.4, H2O.5

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.74, E.75, D.76, R.105, K.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.74 Water bridges: A:E.75 GOL.4: 3 residues within 4Å: Chain A: H.220, H.221, C.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.220, A:C.223 GOL.5: 3 residues within 4Å: Chain A: D.34, S.36, S.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.38 GOL.6: 2 residues within 4Å: Chain A: K.20, A.21 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: Q.41, S.66, Y.67, E.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.41, A:Q.41, A:Y.67

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

EDO.8: 3 residues within 4Å: Chain A: V.72, E.75, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.75, A:E.75, A:R.237

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

TLA.9: 5 residues within 4Å: Chain A: D.176, T.177, F.178, P.179, M.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.177, A:T.177 Water bridges: A:T.177 TLA.10: 2 residues within 4Å: Chain A: D.27, R.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33 Water bridges: A:R.26 Salt bridges: A:R.33 TLA.15: 5 residues within 4Å: Chain C: G.15 Chain D: A.17, U.18, G.19, C.20 No protein-ligand interaction detected (PLIP)

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

PGE.13: 4 residues within 4Å: Chain B: D.27, E.29, A.30, R.33 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.26 PGE.14: 4 residues within 4Å: Chain B: L.70, H.220, H.221, C.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.221

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