SMTL ID : 5lmf.2 (1 other biounit)

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM3 peptide (region 484-500)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: T.150, L.151 Ligands: EDO.7 Ligand excluded by PLIP

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

EDO.2: 5 residues within 4Å: Chain A: F.254, P.255, N.260, E.274, E.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.260, A:E.274 EDO.3: 3 residues within 4Å: Chain A: D.273, A.275, Y.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.273, A:A.275, A:Y.276 Water bridges: A:N.205 EDO.4: 4 residues within 4Å: Chain A: Y.340, E.343, K.344, Q.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.343, A:Q.347 EDO.5: 5 residues within 4Å: Chain A: Y.346, Y.360, R.361, D.362, G.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.360, A:D.362, A:G.363 EDO.6: 8 residues within 4Å: Chain A: S.141, Y.143, T.199, S.200, K.201, P.255, Y.259, Y.276 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.141, A:K.201, A:Y.276, A:Y.276 Water bridges: A:K.201 EDO.7: 5 residues within 4Å: Chain A: K.148, P.149, T.150, H.262 Ligands: CL.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Charenton, C. et al., A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

DNA topoisomerase 2-associated protein PAT1: A
mRNA decapping protein 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

DNA topoisomerase 2-associated protein PAT1

mRNA decapping protein 2

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