SMTL ID : 8ssw.1

Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: N.24, T.25, G.26, I.27, F.51, Y.69, R.71, P.72, T.73, Q.76, Q.94, T.95, G.96, S.97, G.98, K.99, T.100 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.24, A:I.27, A:T.73, A:Q.76, A:Q.76, A:G.96, A:S.97, A:G.98, A:K.99, A:T.100, A:T.100, A:T.100 Water bridges: A:K.99, A:T.100, A:A.101, A:D.216, A:E.217 Salt bridges: A:K.99 pi-Stacking: A:Y.69, A:Y.69 ADP.3: 18 residues within 4Å: Chain B: N.24, T.25, G.26, I.27, F.29, F.51, Y.69, R.71, P.72, T.73, Q.76, Q.94, T.95, G.96, S.97, G.98, K.99, T.100 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:N.24, B:N.24, B:I.27, B:Y.69, B:T.73, B:Q.76, B:Q.76, B:G.96, B:S.97, B:G.98, B:K.99, B:T.100, B:T.100, B:T.100 Water bridges: B:R.71, B:T.95, B:K.99, B:K.99, B:A.101 Salt bridges: B:K.99 pi-Stacking: B:Y.69, B:Y.69

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.100, D.216, E.217 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: N.420 No protein-ligand interaction detected (PLIP)

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

EDO.4: 4 residues within 4Å: Chain C: A.8, U.9 Chain D: G.12, C.13 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain B: N.420 Chain C: U.6, C.7 Chain D: A.14, A.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.420 EDO.7: 5 residues within 4Å: Chain C: U.9, U.10 Chain D: A.15, G.16, A.17 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain C: C.13 Chain D: C.13, A.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, H. et al., Crystal structure of DEAD-box RNA helicase DDX3X in complex with ADP at pre-unwound state. To be published

Release Date

2024-05-22

Peptides

ATP-dependent RNA helicase DDX3X: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA helicase DDX3X

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