SMTL ID : 5osy.1

Human Decapping Scavenger enzyme (hDcpS) in complex with m7G(5'S)ppSp(5'S)G mRNA 5' cap analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x AJQ: [(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-[[[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl]oxy-phosphinic acid(Non-covalent)

AJQ.1: 26 residues within 4Å: Chain A: R.18, D.23, I.25, F.27, E.49, K.106, Y.107, W.139, E.149, R.152, P.168, D.169, L.170, K.171, Y.181, I.183, H.232, S.236, Y.237, H.243, P.252, R.258 Chain B: R.22, K.24, N.74, Y.77 29 PLIP interactions: 3 interactions with chain B, 26 interactions with chain A Hydrogen bonds: B:R.22, B:K.24, B:N.74, A:R.18, A:R.18, A:K.106, A:Y.107, A:Y.107, A:R.152, A:P.168, A:D.169, A:L.170, A:K.171, A:K.171, A:Y.181, A:S.236, A:Y.237, A:R.258, A:R.258 Water bridges: A:K.171, A:K.171, A:Y.181, A:H.232 Salt bridges: A:D.23, A:E.49, A:E.149 pi-Stacking: A:F.27, A:W.139, A:W.139 AJQ.2: 8 residues within 4Å: Chain B: W.139, I.143, E.149, R.152, D.169, L.170, S.236, Y.237 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.152 Water bridges: B:W.139, B:L.170, B:L.170, B:L.170, B:L.170, B:S.236, B:S.236 Salt bridges: B:E.149 pi-Stacking: B:W.139, B:W.139, B:W.139

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: L.114, R.116 Chain B: L.209, L.227, V.229, L.261, L.262, A.263 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.229, B:L.262, B:A.263 GOL.4: 2 residues within 4Å: Chain B: Q.110, D.288 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.288 GOL.5: 5 residues within 4Å: Chain B: K.15, E.101, L.104, Q.105, L.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.15, B:K.15 GOL.6: 6 residues within 4Å: Chain A: A.251, S.254, G.255 Chain B: E.250, S.254, G.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.254 Water bridges: B:R.228 GOL.7: 7 residues within 4Å: Chain A: L.114, I.115, R.116 Chain B: Q.213, G.224, D.225 Ligands: GOL.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.213, B:Q.213, A:L.114 Water bridges: A:R.116, A:R.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wojtczak, B.A. et al., 5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes. J. Am. Chem. Soc. (2018)

Release Date

2018-05-02

Peptides

m7GpppX diphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

m7GpppX diphosphatase

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