SMTL ID : 5kq4.1

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic cap analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x 6VQ: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate(Non-covalent)

6VQ.1: 9 residues within 4Å: Chain C: W.122, K.123, S.125, S.126, G.127, K.134, R.172, Q.174, Y.225 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.126, C:G.127, C:G.127, C:K.134, C:Q.174, C:Y.225 pi-Stacking: C:W.122, C:W.122, C:Y.225, C:Y.225 pi-Cation interactions: C:W.122, C:W.122 6VQ.2: 12 residues within 4Å: Chain F: E.44, W.48, D.52, D.93, F.94, Y.97, K.98, R.100, K.132, R.172, Y.225, M.226 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:W.48, F:K.98, F:R.100, F:R.100, F:Y.225 Salt bridges: F:D.52, F:D.93, F:K.98, F:K.98, F:K.132 pi-Stacking: F:W.48, F:W.48, F:W.48, F:Y.97, F:Y.97, F:Y.225, F:Y.225 pi-Cation interactions: F:W.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mugridge, J.S. et al., Structural basis of mRNA-cap recognition by Dcp1-Dcp2. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-10-05

Peptides

mRNA-decapping enzyme subunit 1: AD
Proline-rich nuclear receptor coactivator 2: BE
mRNA decapping complex subunit 2: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D
A

B
F

E
C

C
E

F
B

mRNA-decapping enzyme subunit 1

Proline-rich nuclear receptor coactivator 2

mRNA decapping complex subunit 2

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