SMTL ID : 6ox2.2 (1 other biounit)

SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: H.8 Chain B: R.80, E.108, E.109, F.111, P.185, T.258, R.259, D.280, M.281, C.282, N.283, H.284, Y.318, S.330, F.332, F.334 Ligands: GOL.10 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:H.284, B:H.284, B:Y.318, B:G.331 Water bridges: B:E.109, B:D.189, B:T.258 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.2: 5 residues within 4Å: Chain B: A.365, A.384, Q.385, I.413, G.417 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.384 EDO.3: 5 residues within 4Å: Chain B: L.346, G.347, F.393, F.434, R.438 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.347, B:R.438 EDO.4: 7 residues within 4Å: Chain B: P.46, E.51, E.54, H.209, F.212, S.213, K.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.213, B:K.216 EDO.5: 3 residues within 4Å: Chain B: D.86, W.90, E.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.86, B:D.86, B:E.93 EDO.6: 3 residues within 4Å: Chain B: E.360, A.363, R.364 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.360 EDO.7: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.71 EDO.8: 4 residues within 4Å: Chain B: P.185, S.186, E.187 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.186, B:S.186, B:E.187 Water bridges: B:E.187 EDO.9: 5 residues within 4Å: Chain B: P.129, R.130, K.131, D.297, D.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.131, B:D.298

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain B: R.80, G.110, F.111 Ligands: SAH.1, EDO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.80, B:R.80, B:F.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., Structural basis for the target specificity of actin histidine methyltransferase SETD3. Nat Commun (2019)

Release Date

2019-08-21

Peptides

Actin Peptide: A
Histone-lysine N-methyltransferase setd3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

B
B

Actin Peptide

Histone-lysine N-methyltransferase setd3

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