SMTL ID : 8szq.1

Cat DHX9 bound to ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: L.240, T.265, G.266, C.267, G.268, K.269, T.270, T.271, R.308, E.364, F.551, S.571, T.573, N.575 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.271, A:E.364, A:T.573, A:N.575 Water bridges: A:T.265, A:K.269, A:K.269, A:T.270, A:R.308, A:R.308, A:T.570, A:S.571 Salt bridges: A:K.269 pi-Stacking: A:F.551 pi-Cation interactions: A:R.308, A:R.308

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.270, D.363, E.364 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.270, A:E.364, H2O.1, H2O.1, H2O.1

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: R.326, T.342, G.344, V.345, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.344, A:V.345, A:N.371 Salt bridges: A:R.326, A:R.348 SO4.4: 4 residues within 4Å: Chain A: P.836, R.992, P.993, S.994 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.994, A:S.994, A:S.994 Water bridges: A:R.763, A:D.837 Salt bridges: A:R.992 SO4.5: 5 residues within 4Å: Chain A: P.297, R.298, E.367, D.369, E.644 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.297, A:D.369, A:E.644 Salt bridges: A:R.298 SO4.6: 5 residues within 4Å: Chain A: G.511, W.512, H.539, S.540, K.587 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.512, A:S.540, A:S.540, A:Q.541 Salt bridges: A:K.587 SO4.7: 7 residues within 4Å: Chain A: R.715, F.849, Y.852, F.922, S.924, K.925, R.956 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.715, A:R.956 SO4.8: 7 residues within 4Å: Chain A: G.263, A.264, T.265, A.396, T.397, Q.612, R.616 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.265, A:T.265, A:T.397, A:T.397, A:Q.612 Salt bridges: A:R.616 SO4.9: 3 residues within 4Å: Chain A: K.750, R.751, K.876 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.751 Salt bridges: A:R.751, A:K.876 SO4.10: 6 residues within 4Å: Chain A: G.344, L.347, N.371, E.652, I.653, S.656 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.371, A:N.371

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

EDO.11: 6 residues within 4Å: Chain A: R.763, D.841, I.844, L.913, Q.918, S.991 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.763, A:D.841, A:D.841, A:Q.918 EDO.12: 4 residues within 4Å: Chain A: F.327, E.328, S.329, E.807 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.327, A:S.329, A:S.329 Water bridges: A:E.328 EDO.13: 5 residues within 4Å: Chain A: E.481, K.482, K.585, T.602, W.604 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.585, A:T.602, A:W.604 EDO.14: 5 residues within 4Å: Chain A: V.728, A.731, Q.829, F.831, N.839 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.829 Water bridges: A:A.731, A:Q.829 EDO.15: 3 residues within 4Å: Chain A: G.666, I.682, E.685 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.666

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, Y.T. et al., Crystal structures of the DExH-box RNA helicase DHX9. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-08-02

Peptides

RNA helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA helicase

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