SMTL ID : 9d5k.1

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing an expanded cytidine analog at the -1 position of the guide strand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 18 residues within 4Å: Chain A: N.177, I.183, R.186, R.187, T.299, K.305, R.308, G.316, S.317, K.415, Y.444, K.448, Y.454, K.458, W.473, E.475, K.476 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.177, A:R.186, A:S.317, A:K.476 Salt bridges: A:R.186, A:R.187, A:R.187, A:K.305, A:K.305, A:R.308, A:R.308, A:R.308, A:K.415, A:K.448, A:K.448, A:K.448, A:K.458, A:K.476 IHP.4: 19 residues within 4Å: Chain B: N.177, I.183, R.186, R.187, T.299, K.305, R.308, G.316, S.317, K.415, Y.444, K.448, Y.454, K.458, W.473, V.474, E.475, K.476, Q.480 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.177, B:S.317, B:K.476, B:Q.480 Salt bridges: B:R.186, B:R.187, B:R.187, B:K.305, B:K.305, B:R.308, B:R.308, B:R.308, B:K.415, B:K.448, B:K.448, B:K.448, B:K.458, B:K.476

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.180, E.182, C.237, K.269, C.302 Chain C: X.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.180, A:C.237, A:C.302 ZN.5: 5 residues within 4Å: Chain B: H.180, E.182, C.237, K.269, C.302 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.180, B:C.237, B:C.302, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.475, K.476 Ligands: IHP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manjunath, A. et al., Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5'-G A Sites. Biomolecules (2024)

Release Date

2024-11-06

Peptides

Isoform 4 of Double-stranded RNA-specific editase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 4 of Double-stranded RNA-specific editase 1

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