SMTL ID : 9op3.1

Structure of Human ADAR2-R2D complexed with dsRNA containing 8-azaN and 2'-Deoxy-2'-fluorouridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 19 residues within 4Å: Chain A: N.178, D.179, I.184, R.187, R.188, T.300, K.306, R.309, G.317, S.318, K.416, Y.445, K.449, Y.455, K.459, E.476, K.477, D.482 Ligands: NA.6 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:N.178, A:R.187, A:S.318, A:E.476, A:E.476, A:K.477 Water bridges: A:R.309, A:R.309, A:Y.455, A:Y.455 Salt bridges: A:R.187, A:R.188, A:R.188, A:K.306, A:K.306, A:R.309, A:R.309, A:K.416, A:K.449, A:K.449, A:K.449, A:K.459, A:K.477, A:K.477 IHP.7: 20 residues within 4Å: Chain B: N.178, D.179, I.184, R.187, R.188, T.300, K.306, R.309, G.317, S.318, K.416, Y.445, K.449, Y.455, K.459, W.474, V.475, E.476, K.477, D.482 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.178, B:R.187, B:S.318, B:W.474, B:K.477, B:K.477 Salt bridges: B:R.187, B:R.188, B:R.188, B:K.306, B:K.306, B:R.309, B:R.309, B:R.309, B:K.416, B:K.416, B:K.449, B:K.449, B:K.449, B:K.459

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.181, E.183, C.238, K.270, C.303 Chain C: X.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.181, A:C.238, A:C.303 ZN.8: 5 residues within 4Å: Chain B: H.181, E.183, C.238, K.270, C.303 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.181, B:C.238, B:C.303, H2O.2

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

EDO.3: 6 residues within 4Å: Chain A: K.137, V.138, T.235, R.242, R.377 Chain C: X.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.235, A:T.235, A:R.242, A:R.377 EDO.4: 3 residues within 4Å: Chain A: R.192, R.413, A.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.192 EDO.5: 4 residues within 4Å: Chain A: D.112, S.115, S.372, N.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.115, A:S.115, A:S.372, A:N.373, A:N.373

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: E.476 Ligands: IHP.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.476, A:E.476, A:K.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, K.B. et al., Control of ADAR2 Dimerization and RNA Editing Efficiency by Site-specific 2'-Fluoro Modification of Guide RNAs. To Be Published

Release Date

2025-10-08

Peptides

Double-stranded RNA-specific editase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Double-stranded RNA-specific editase 1

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