SMTL ID : 6s8s.1 (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

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

PO4.1: 5 residues within 4Å: Chain A: R.29, Q.30, H.33 Chain B: P.16, F.20 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.29, A:Q.30 Salt bridges: A:H.33 Water bridges: B:N.25, B:N.25 PO4.2: 3 residues within 4Å: Chain A: S.53, S.54, K.77 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.54 Water bridges: A:S.53, A:Q.55 Salt bridges: A:K.77 PO4.3: 4 residues within 4Å: Chain A: K.77, M.78, R.79, H.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.79 Salt bridges: A:H.82 PO4.4: 4 residues within 4Å: Chain A: F.39, S.40, Y.69 Ligands: CXS.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.40 PO4.5: 6 residues within 4Å: Chain A: N.52, D.102, P.122, K.123, L.124, T.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.123, A:L.124, A:L.124 Water bridges: A:D.102

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

CXS.6: 5 residues within 4Å: Chain A: R.153, F.154 Chain B: E.37, I.38, Y.41 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.41 Salt bridges: A:R.153 CXS.7: 9 residues within 4Å: Chain A: F.39, S.40, R.41, L.42, Q.43, Y.69, R.96, K.176 Ligands: PO4.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.69, A:Y.69 Hydrogen bonds: A:F.39 Water bridges: A:I.44 Salt bridges: A:K.176 CXS.8: 10 residues within 4Å: Chain A: L.38, R.41, L.42, I.170, P.171, S.172, N.173, I.174 Chain B: D.19, F.22 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.38, A:R.41, A:L.42, A:I.170, A:I.170, A:I.174, B:F.22 Salt bridges: A:R.41

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
A

B
B

Probable ATP-dependent RNA helicase DDX6

Enhancer of mRNA-decapping protein 3

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