SMTL ID : 7kfn.1

Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing a 2'-deoxy Benner's Base Z opposite the edited base

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 18 residues within 4Å: Chain A: N.93, I.99, R.102, R.103, T.215, K.221, R.224, G.232, S.233, K.331, Y.360, K.364, Y.370, K.374, W.389, E.391, K.392, D.397 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:N.93, A:S.233, A:K.392, A:D.397 Water bridges: A:D.94, A:R.102, A:R.102, A:R.103, A:R.103, A:R.103, A:R.224, A:R.224, A:K.331, A:Y.360, A:Y.360, A:Y.370, A:Y.370, A:V.390, A:D.397 Salt bridges: A:R.102, A:R.103, A:R.103, A:K.221, A:K.221, A:R.224, A:R.224, A:K.331, A:K.364, A:K.364, A:K.364, A:K.374, A:K.392 IHP.3: 19 residues within 4Å: Chain D: N.93, D.94, I.99, R.102, R.103, T.215, K.221, R.224, G.232, S.233, K.331, Y.360, K.364, Y.370, K.374, W.389, E.391, K.392, D.397 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:N.93, D:S.233, D:K.392 Water bridges: D:N.93, D:R.102, D:R.102, D:R.103, D:R.103, D:K.221, D:L.234, D:Y.360, D:Y.370, D:K.392 Salt bridges: D:R.102, D:R.103, D:R.103, D:K.221, D:K.221, D:R.224, D:R.224, D:K.331, D:K.364, D:K.364, D:K.364, D:K.374, D:K.392, D:K.392

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.96, E.98, C.153, K.185, C.218 Chain B: X.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:C.153, A:C.218 ZN.4: 5 residues within 4Å: Chain D: H.96, E.98, C.153, K.185, C.218 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.96, D:C.153, D:C.218, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doherty, E.E. et al., Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position. J.Am.Chem.Soc. (2021)

Release Date

2021-06-16

Peptides

Double-stranded RNA-specific editase 1: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

Double-stranded RNA-specific editase 1

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