SMTL ID : 5nkm.2 (2 other biounits)

SMG8-SMG9 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: E.106, E.135, R.138, F.139, K.142 Chain B: K.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.106, A:K.142 EDO.2: 6 residues within 4Å: Chain A: K.21, V.166, E.305, I.306, S.307, N.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.305, A:S.307, A:S.307, A:N.310 EDO.6: 13 residues within 4Å: Chain A: I.339, I.342, Q.343, H.346, V.398, V.399, G.400, V.401 Chain B: Q.157, I.158, R.159, W.210, T.296 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.346, A:G.400, B:Q.157 EDO.7: 11 residues within 4Å: Chain B: A.127, L.130, Y.131, A.155, E.156, Q.157, I.158, R.159, T.175, W.210, L.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.130, B:E.156, B:R.159, B:R.159

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 13 residues within 4Å: Chain A: K.30, D.31, Y.32, D.81, D.82, V.83, I.86 Chain B: H.143, Y.144, D.145, K.146, R.197, L.200 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.144, B:R.197, A:D.31, A:D.31 Water bridges: B:R.197

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: Y.44, D.69, D.70, V.292 No protein-ligand interaction detected (PLIP) PEG.5: 9 residues within 4Å: Chain A: K.141, N.144, S.145, I.148, Y.229, D.230, C.234, S.237, S.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.144, A:D.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins. RNA (2017)

Release Date

2017-04-19

Peptides

Protein smg-8: A
Protein smg-9: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Protein smg-8

Protein smg-9

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