SMTL ID : 6am0.1

Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.134, E.148, E.197 Ligands: 6VQ.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.148

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.2: 13 residues within 4Å: Chain A: W.49, T.52, D.53, K.126, H.127, R.132, K.134, H.194, K.195, N.196, E.197, F.223 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.49, A:R.132, A:N.196 Salt bridges: A:D.53, A:K.134, A:K.134 pi-Stacking: A:W.49, A:W.49, A:W.49, A:F.223, A:F.223 pi-Cation interactions: A:K.126 6VQ.3: 13 residues within 4Å: Chain E: W.49, D.53, K.100, H.127, R.132, K.134, E.151, K.174, F.176, H.194, N.196, E.197, F.223 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:K.100, E:R.132, E:K.134, E:K.174, E:N.196, E:N.196, E:N.196 Salt bridges: E:D.53, E:K.134, E:K.134, E:K.174 pi-Stacking: E:W.49, E:W.49, E:F.223, E:F.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mugridge, J.S. et al., Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun (2018)

Release Date

2018-03-21

Peptides

KLLA0F23980p: AE
KLLA0E01827p: BF
KLLA0A01474p: CG
KLLA0A11308p: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

KLLA0F23980p

KLLA0E01827p

KLLA0A01474p

KLLA0A11308p

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