SMTL ID : 6s8s.2 (1 other biounit)

Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-mer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: S.53, S.54, Q.55, K.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.54 Salt bridges: A:K.77 PO4.2: 4 residues within 4Å: Chain A: R.91, D.109, I.110, Q.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.111 Water bridges: A:R.91, A:A.112, A:A.112 Salt bridges: A:R.91 PO4.3: 3 residues within 4Å: Chain A: M.78, R.79, H.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79, A:R.79 Salt bridges: A:H.82 PO4.6: 5 residues within 4Å: Chain A: S.172 Chain B: D.21, F.22, E.23 Ligands: CXS.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:P.171, A:S.172 Hydrogen bonds: B:D.21, B:F.22, B:E.23

2 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.4: 10 residues within 4Å: Chain A: L.38, R.41, L.42, I.170, P.171, S.172, N.173, I.174 Chain B: F.22 Ligands: PO4.6 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.38, A:R.41, A:L.42, A:I.170, A:I.174, B:F.22 Hydrogen bonds: A:N.173 Water bridges: B:D.19 CXS.5: 8 residues within 4Å: Chain A: F.39, S.40, R.41, L.42, Q.43, Y.69, R.96, K.176 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.69 Hydrogen bonds: A:F.39 Water bridges: A:R.41 Salt bridges: A:K.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peter, D. et al., Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression. Genes Dev. (2019)

Release Date

2019-09-04

Peptides

Probable ATP-dependent RNA helicase DDX6: A
Enhancer of mRNA-decapping protein 3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Probable ATP-dependent RNA helicase DDX6

Enhancer of mRNA-decapping protein 3

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