SMTL ID : 5j3t.1

Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 6 residues within 4Å: Chain A: S.34, H.35, T.56, R.74 Chain B: N.22, L.23 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.35, A:R.74, A:R.74, B:N.22 Water bridges: A:T.56 FMT.2: 7 residues within 4Å: Chain A: F.83, I.84, N.85, H.86, N.89, H.99, R.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.85, A:H.86, A:H.86, A:N.89, A:H.99 FMT.3: 5 residues within 4Å: Chain B: G.124, F.125, K.127, M.221, F.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.125, B:F.125 FMT.4: 3 residues within 4Å: Chain B: N.157, N.159, E.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.157, B:N.157 FMT.5: 4 residues within 4Å: Chain B: S.194, K.195, I.196, E.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.196

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain B: Y.92 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valkov, E. et al., Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-05-18

Peptides

mRNA-decapping enzyme subunit 1: A
mRNA decapping complex subunit 2: B
Edc1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

mRNA-decapping enzyme subunit 1

mRNA decapping complex subunit 2

Edc1

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