SMTL ID : 6ozj.1

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: Y.79, E.80, D.81, K.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.79, A:D.81 Water bridges: A:E.80 GOL.2: 5 residues within 4Å: Chain A: V.105, V.108, Q.109, L.145, T.146 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.109, A:Q.109, A:T.146 GOL.3: 7 residues within 4Å: Chain A: F.42, S.43, G.44, L.45, Q.46, Y.72, P.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.44, A:L.45, A:L.45, A:Q.46 Water bridges: A:F.42 GOL.4: 5 residues within 4Å: Chain A: E.20, L.24, F.98, H.141, L.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.20, A:H.141

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

EDO.5: 2 residues within 4Å: Chain A: K.47, Q.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.47, A:K.47 EDO.6: 3 residues within 4Å: Chain A: S.71, K.76, V.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.71, A:S.71 EDO.8: 3 residues within 4Å: Chain B: R.237, Q.238 Chain C: C.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.237, B:R.237, B:Q.238 Water bridges: B:Q.238 EDO.9: 3 residues within 4Å: Chain B: A.22, K.25, A.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.22

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

PGE.7: 5 residues within 4Å: Chain A: P.73, H.225, H.226, C.228, R.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.229

2 x K: POTASSIUM ION(Non-functional Binders)

K.10: 2 residues within 4Å: Chain C: U.22 Chain D: U.14 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain D: U.18 No protein-ligand interaction detected (PLIP)

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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