SMTL ID : 8szs.1

Cat DHX9 bound to GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 16 residues within 4Å: Chain A: L.240, A.264, T.265, G.266, C.267, G.268, K.269, T.270, T.271, R.308, F.551, S.571, T.573, N.575, R.619 Ligands: MG.2 23 PLIP interactions: 23 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:R.308, A:E.364, A:T.573, A:N.575, A:R.619 Water bridges: A:G.263, A:K.269, A:K.269, A:K.269, A:T.270, A:T.570, A:T.573 Salt bridges: A:K.269 pi-Stacking: A:F.551 pi-Cation interactions: A:R.308, A:R.308, A:F.551

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.270, D.363, E.364 Ligands: GDP.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.2

9 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:R.326, A:G.344, A:V.345 Salt bridges: A:R.326, A:R.348 SO4.4: 4 residues within 4Å: Chain A: P.836, R.992, P.993, S.994 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.994 Water bridges: A:D.837, A:D.837, A:D.841, A:D.841, A:N.999 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: 8 residues within 4Å: Chain A: R.715, F.849, Y.852, F.922, A.923, S.924, K.925, R.956 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.924, A:S.924 Salt bridges: A:R.715, A:R.956 SO4.7: 8 residues within 4Å: Chain A: G.263, A.264, T.265, A.396, T.397, T.570, Q.612, R.616 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.265, A:T.265, A:T.397, A:Q.612 Salt bridges: A:R.616 SO4.8: 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 SO4.9: 4 residues within 4Å: Chain A: Q.775, F.831, T.832, N.833 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.775, A:T.832, A:N.833, A:N.833, A:N.833 SO4.10: 6 residues within 4Å: Chain A: G.344, L.347, N.371, E.652, I.653, S.656 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.371 Water bridges: A:N.371, A:S.656 SO4.11: 4 residues within 4Å: Chain A: F.426, R.631, F.634, E.635 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.635 Salt bridges: A:R.631

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

EDO.12: 6 residues within 4Å: Chain A: R.763, D.841, I.844, Q.918, S.991, P.993 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: F.327, E.328, S.329, E.807 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: P.187, Q.188, S.189, P.209, A.288, E.289 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: W.806, K.809, V.810, K.813, T.828 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: V.728, A.731, Q.829, F.831, N.839 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: S.304, E.307, R.544, Q.547, R.548 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: L.220, L.224, L.234, R.237, D.279, R.313 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: L.250, I.253, S.254, D.280, F.281, H.359 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: R.262, T.397, E.414 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: G.666, V.681, I.682, E.685 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: S.247, L.250 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: T.903, R.904 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: E.743, D.766, G.910 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: L.427, N.461, N.480, E.481, E.483, K.585, L.628 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: R.661, G.663, E.699 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: K.482, K.585, T.602, V.603, W.604 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: S.540, T.565, I.567, K.587 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gotur, D. et al., Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9. Slas Discov (2023)

Release Date

2023-09-06

Peptides

RNA helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA helicase

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