SMTL ID : 6ox3.1 (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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: T.12, N.13, K.19 Chain B: N.159, L.273 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.159, B:N.159, A:N.13, A:K.19 Water bridges: B:G.158 GOL.3: 3 residues within 4Å: Chain B: K.131, F.176, W.177 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.131 GOL.4: 5 residues within 4Å: Chain B: E.109, P.185, E.187, Y.188 Ligands: SAH.2 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.109, B:E.187 Water bridges: B:R.80, B:R.80, B:D.189, B:T.258 GOL.5: 5 residues within 4Å: Chain B: I.344, K.345, L.346, R.438, L.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.345, B:R.438, B:R.438 GOL.6: 5 residues within 4Å: Chain A: Y.4 Chain B: Y.293, N.294, L.295, E.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.293, B:L.295, B:E.296

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

SAH.2: 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: GOL.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:H.284, B:H.284, B:Y.318 Water bridges: B:R.80, B:E.109, B:E.109, B:D.189, B:T.258, B:T.258, B:S.330, B:G.331 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.7: 2 residues within 4Å: Chain B: K.454 Ligands: EDO.18 Ligand excluded by PLIP EDO.8: 11 residues within 4Å: Chain B: S.322, N.323, A.324, D.340, R.341, V.342, L.472, E.476, I.479 Ligands: EDO.10, EDO.13 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: D.210, A.324, E.325, I.328, H.329 Ligands: EDO.10, EDO.13 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain B: Q.206, A.207, D.210, A.324, K.343, E.476 Ligands: EDO.8, EDO.9, EDO.13 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: I.367, A.384, Q.385, A.388, I.413 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: D.118, I.119, K.120, D.307, F.308, R.309 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain B: S.322, A.324, E.325, R.341, V.342, K.343 Ligands: EDO.8, EDO.9, EDO.10 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: L.457, H.460, D.461, L.462, K.467 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain B: K.107 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: Y.4, P.5, I.6 Chain B: Q.262, I.263, P.264, V.271 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: N.323, D.340, F.377, G.475, E.478, I.479 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: K.454, L.474, E.478 Ligands: EDO.7 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: T.75, F.76, D.77 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: E.51, E.54, H.209, F.212, S.213, K.216 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: Q.69, Y.226, S.243, F.244 Ligands: EDO.26 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain B: S.370 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: F.333, V.464, K.467, M.468, K.471 Ligands: EDO.28 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: L.405, G.406, D.407, S.408, A.409, R.412 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain B: Y.226, I.229, Q.230, L.240, K.241, D.242, S.243, F.244 Ligands: EDO.22 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: L.346, G.347, F.393, F.434, R.438 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: D.189, G.331, F.332, F.333, V.464, M.468 Ligands: EDO.24 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.29: 5 residues within 4Å: Chain B: V.372, F.373, A.374, S.383, Q.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.374, B:S.383

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
Y

B
A

Actin Peptide

Histone-lysine N-methyltransferase setd3

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