SMTL ID : 9b83.1

Cryo-EM structure of human ADAR1 in complex with dsRNA derived from human GLI1 gene

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 18 residues within 4Å: Chain B: N.1173, I.1179, R.1182, R.1183, K.1305, R.1308, G.1316, A.1317, K.1424, Y.1448, K.1452, Y.1458, K.1462, W.1477, I.1478, S.1479, K.1480, K.1485 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.1173, B:A.1317, B:W.1477, B:K.1480 Salt bridges: B:R.1182, B:R.1182, B:R.1183, B:R.1183, B:K.1305, B:K.1305, B:R.1308, B:K.1424, B:K.1452, B:K.1452, B:K.1452, B:K.1462, B:K.1480, B:K.1485, B:K.1485 IHP.4: 17 residues within 4Å: Chain C: I.1179, R.1182, R.1183, T.1299, K.1305, R.1308, G.1316, A.1317, K.1424, Y.1448, K.1452, Y.1458, K.1462, I.1478, S.1479, K.1480, K.1485 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:A.1317, C:Y.1448, C:Y.1458, C:K.1480 Salt bridges: C:R.1182, C:R.1182, C:R.1183, C:R.1183, C:K.1305, C:K.1305, C:R.1308, C:R.1308, C:K.1452, C:K.1452, C:K.1452, C:K.1453, C:K.1462, C:K.1480, C:K.1485

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: X.12 Chain B: H.1176, C.1232, C.1302 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.1176, B:C.1232, B:C.1302 ZN.3: 4 residues within 4Å: Chain B: H.1254, C.1347, C.1348, H.1369 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.1254, B:C.1347, B:C.1348, B:H.1369 ZN.5: 4 residues within 4Å: Chain C: H.1176, E.1178, C.1232, C.1302 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.1176, C:C.1232, C:C.1302 ZN.6: 5 residues within 4Å: Chain C: H.1254, T.1343, C.1347, C.1348, H.1369 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.1254, C:C.1347, C:C.1348, C:H.1369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., Biochemical profiling and structural basis of ADAR1-mediated RNA editing. Mol.Cell (2025)

Release Date

2025-03-26

Peptides

Maltodextrin-binding protein,Double-stranded RNA-specific adenosine deaminase: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

Maltodextrin-binding protein,Double-stranded RNA-specific adenosine deaminase

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