SMTL ID : 6hyt.1 (3 other biounits)

Crystal structure of DHX8 helicase domain bound to ADP at 2.3 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: L.18, E.42, T.43, G.44, S.45, G.46, K.47, T.48, T.49, S.78, R.82, F.278, T.300, D.302, R.346 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.44, A:S.45, A:G.46, A:K.47, A:T.48, A:T.49, A:S.78, A:T.300, A:D.302, A:R.346, A:R.346 Water bridges: A:K.47, A:K.47, A:T.48, A:T.48, A:T.300, A:D.302 Salt bridges: A:K.47 pi-Stacking: A:F.278

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.48, D.138 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.48, H2O.1, H2O.2, H2O.3, H2O.4

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

EDO.3: 8 residues within 4Å: Chain A: F.471, K.485, D.494, T.497, L.498, S.591, A.593, E.617 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.485, A:K.485, A:A.593, A:E.617 EDO.4: 6 residues within 4Å: Chain A: H.221, P.226, P.258, G.284, S.285, R.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.285 EDO.5: 3 residues within 4Å: Chain A: H.589, M.615, R.616 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.615

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 3 residues within 4Å: Chain A: L.23, F.188, T.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.189 pi-Cation interactions: A:F.188 DMS.7: 4 residues within 4Å: Chain A: M.411, E.412, Y.415, D.421 No protein-ligand interaction detected (PLIP) DMS.8: 3 residues within 4Å: Chain A: A.58, G.59, R.63 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.60

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 6 residues within 4Å: Chain A: L.200, T.202, T.216, Y.353, R.354, L.355 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.353 Hydrogen bonds: A:L.200

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: Y.21, K.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Felisberto-Rodrigues, C. et al., Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release. Biochem.J. (2019)

Release Date

2019-08-28

Peptides

ATP-dependent RNA helicase DHX8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent RNA helicase DHX8

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