SMTL ID : 8szp.2 (1 other biounit)

Human DHX9 bound to ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 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, R.418, F.551, T.573, N.575, R.619 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:T.271, A:T.271, A:R.308, A:R.418, A:N.575, A:N.575, A:R.619 Water bridges: A:T.265, A:K.269, A:T.270 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

6 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.342, A:T.342, A:G.344, A:V.345 Water bridges: A:R.326, A:R.326 Salt bridges: A:R.348 SO4.4: 4 residues within 4Å: Chain A: D.841, R.992, P.993, S.994 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.994, A:S.994 Water bridges: A:D.837, A:D.837 Salt bridges: A:R.992 SO4.5: 6 residues within 4Å: Chain A: G.664, I.665, G.666, Q.667, E.685 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.665, A:G.666, A:Q.667 SO4.6: 6 residues within 4Å: Chain A: H.539, S.540, T.565, N.566, I.567 Ligands: SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.540, A:S.540, A:T.565, A:T.565 SO4.7: 2 residues within 4Å: Chain A: T.903, R.904 No protein-ligand interaction detected (PLIP) SO4.8: 8 residues within 4Å: Chain A: L.509, P.510, G.511, T.565, N.566, Q.586, K.587 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.511, A:N.566, A:K.587

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

EDO.9: 7 residues within 4Å: Chain A: R.763, D.841, I.844, L.913, Q.918, S.991, L.1000 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.763, A:D.841, A:Q.918, A:S.991 EDO.10: 2 residues within 4Å: Chain A: Y.727, S.974 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: V.681, I.682, E.685 Ligands: SO4.5 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: R.298, R.299, S.540 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.299, A:S.540, A:S.540 EDO.13: 2 residues within 4Å: Chain A: I.149, E.947 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.947, A:E.947 EDO.14: 1 residues within 4Å: Chain A: H.527 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: R.262, T.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.262 EDO.16: 2 residues within 4Å: Chain A: N.371, E.652 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.371 Water bridges: A:E.652, A:A.708

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

ATP-dependent RNA helicase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

ATP-dependent RNA helicase A

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