SMTL ID : 6ox1.2 (1 other biounit)

SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: 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 Chain B: H.8 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:F.111, A:F.111, A:N.283, A:H.284, A:H.284 Water bridges: A:R.80, A:E.109, A:E.109, A:D.189, A:D.189, A:T.258, A:S.330, A:G.331 Salt bridges: A:R.80, A:R.259 pi-Stacking: A:F.332, A:F.332

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

EDO.2: 6 residues within 4Å: Chain A: A.365, A.384, Q.385, A.388, I.413, G.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.365, A:A.384 EDO.3: 3 residues within 4Å: Chain A: L.346, G.347, R.438 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.347, A:R.438, A:R.438 EDO.4: 6 residues within 4Å: Chain A: P.46, E.51, E.54, F.212, S.213, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.54, A:S.213, A:K.216 Water bridges: A:E.54 EDO.5: 5 residues within 4Å: Chain A: D.86, K.89, W.90, E.93, P.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.86, A:D.86, A:K.89, A:E.93 EDO.6: 2 residues within 4Å: Chain A: E.360, A.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.360 EDO.7: 3 residues within 4Å: Chain A: R.66, K.67, Q.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.66 EDO.8: 3 residues within 4Å: Chain A: P.185, S.186, E.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.186, A:S.186, A:E.187 Water bridges: A:R.80

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

Histone-lysine N-methyltransferase setd3: A
Actin, cytoplasmic 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
Z

Histone-lysine N-methyltransferase setd3

Actin, cytoplasmic 1

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