SMTL ID : 6ox3.2 (1 other biounit)

SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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: K.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: PGE.14 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:T.258, B:T.258, B:N.283, B:H.284, B:H.284, B:Y.318 Water bridges: B:E.109, B:E.109, B:D.189, B:S.330, B:G.331 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.2: 4 residues within 4Å: Chain A: E.7 Chain B: I.289, G.319, T.320 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.7, B:T.320 EDO.3: 6 residues within 4Å: Chain B: A.365, A.384, A.388, I.413, F.414, G.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.413 Water bridges: B:G.417 EDO.4: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.69 EDO.5: 4 residues within 4Å: Chain B: Y.188, D.189, R.465 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.188, B:R.465 Water bridges: B:D.189, B:D.189 EDO.6: 4 residues within 4Å: Chain B: L.346, G.347, F.393, R.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.347, B:R.438, B:R.438 EDO.7: 3 residues within 4Å: Chain B: M.88, K.89, S.92 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain B: S.322, N.323, A.324, D.340, R.341, L.472, G.475, E.476 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.323, B:A.324 EDO.9: 3 residues within 4Å: Chain B: H.339, R.341, H.376 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.339 EDO.10: 4 residues within 4Å: Chain B: P.185, S.186, E.187 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.186, B:S.186, B:E.187 Water bridges: B:R.80 EDO.11: 4 residues within 4Å: Chain B: Q.69, Y.226, S.243, F.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.69, B:F.244 EDO.12: 7 residues within 4Å: Chain B: H.403, R.412, T.415, L.416, F.421, P.422, V.423 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.403, B:T.415, B:F.421 EDO.13: 1 residues within 4Å: Chain B: R.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.299, B:R.299

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 9 residues within 4Å: Chain B: D.189, G.331, F.332, F.333, V.464, K.467, M.468, K.471 Ligands: SAH.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.109, B:F.333 Water bridges: B:D.189

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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