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

Crystal structure of DHX8 helicase domain bound to ADP at 2.6 angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 17 PLIP interactions: 17 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 Water bridges: A:Q.14, A:K.47, A:T.48, A:T.48, A:R.82, A:D.138 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, E.139 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.48, H2O.1, H2O.1, H2O.2, H2O.3

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

DMS.3: 3 residues within 4Å: Chain A: M.411, E.412, Y.415 No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain A: 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: 9 residues within 4Å: Chain A: R.121, S.380, L.383, S.384, M.433, A.434, F.436, L.438, C.443 No protein-ligand interaction detected (PLIP) DMS.9: 2 residues within 4Å: Chain A: A.58, Y.60 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.60 DMS.10: 5 residues within 4Å: Chain A: P.310, G.311, F.312, P.331, M.365 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain A: R.100, R.121, P.437 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.439 DMS.12: 3 residues within 4Å: Chain A: L.480, Q.483, K.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.484 DMS.13: 3 residues within 4Å: Chain A: H.589, V.608, R.616 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.589

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

EDO.4: 6 residues within 4Å: Chain A: F.471, K.485, D.494, T.497, L.498, E.617 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.494 Water bridges: A:E.617 EDO.5: 2 residues within 4Å: Chain A: G.284, R.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.284 Water bridges: A:H.221, A:R.286

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

ACT.8: 5 residues within 4Å: Chain A: L.200, T.202, T.216, Y.353, R.354 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.353 Hydrogen bonds: A:L.200

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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