SMTL ID : 6uv2.1

Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: F.65, F.83, E.85, P.86, T.87, Q.90, Q.108, T.109, G.110, S.111, G.112, K.113, T.114, L.115, D.375, R.403, S.404 Ligands: BEF.2, MG.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:E.85, A:T.87, A:Q.90, A:Q.108, A:G.110, A:S.111, A:G.112, A:K.113, A:T.114, A:T.114, A:T.114, A:D.375, A:S.404 Water bridges: A:E.85, A:L.115, A:Q.151, A:Q.151, A:R.403 Salt bridges: A:K.113, A:R.403, A:R.403 pi-Stacking: A:F.83, A:F.83

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 10 residues within 4Å: Chain A: T.109, G.110, K.113, E.218, A.249, G.373, R.400, R.403 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.114, D.217, E.218 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: R.101, D.102, R.264, D.265 Ligands: MG.5 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain A: K.24, G.100, R.101, D.102, R.242, Q.243 Ligands: MG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.100, A:D.102 MG.6: 3 residues within 4Å: Chain A: N.273, E.275, S.277 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.273, A:E.275, A:S.277, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, T.D. et al., RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis. Cell Rep (2019)

Release Date

2020-01-01

Peptides

Probable ATP-dependent RNA helicase DDX17: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable ATP-dependent RNA helicase DDX17

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