SMTL ID : 6mbj.1 (1 other biounit)

SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.12, N.13 Chain B: G.158, N.159 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain B: K.454, L.457, K.471 Ligands: EDO.13 Ligand excluded by PLIP EDO.4: 12 residues within 4Å: Chain B: S.322, N.323, A.324, D.340, R.341, V.342, L.472, G.475, E.476, I.479 Ligands: EDO.6, EDO.9 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain B: D.210, A.324, E.325, I.328, H.329 Ligands: EDO.6, EDO.9 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain B: Q.206, A.207, D.210, A.324, K.343, E.476 Ligands: EDO.4, EDO.5, EDO.9 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain B: A.365, A.384, Q.385, I.413, G.417 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: D.118, I.119, K.120, D.307, F.308, R.309 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain B: S.322, A.324, E.325, R.341, V.342, K.343 Ligands: EDO.4, EDO.5, EDO.6 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: L.457, H.460, D.461, L.462, K.467 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Y.4, P.5 Chain B: Q.262, I.263, P.264, V.271 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: D.340, F.377, G.475, E.478, I.479 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: E.478 Ligands: EDO.3, EDO.12 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: A.45, E.51, E.54, H.209, F.212, S.213, K.216 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: Q.69, Y.226, S.243, F.244 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain B: S.370 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: R.59, T.60, E.196 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: F.333, V.464, M.468, K.471 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: L.405, G.406, D.407, S.408, A.409, R.412 Ligand excluded by PLIP

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

SAH.2: 19 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, G.331, F.332, F.334 Ligands: GOL.22 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:F.111, B:N.283, B:H.284, B:H.284, B:Y.318, B:G.331 Water bridges: B:R.80, B:E.109, B:E.109, B:T.258, B:T.258 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 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.22: 5 residues within 4Å: Chain B: E.109, P.185, E.187, Y.188 Ligands: SAH.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.109, B:E.187 Water bridges: B:F.111, B:D.189, B:T.258 GOL.23: 6 residues within 4Å: Chain B: K.343, I.344, K.345, L.346, R.438, L.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.343, B:K.345, B:R.438

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

ACT.24: 5 residues within 4Å: Chain B: V.372, F.373, A.374, S.383, Q.385 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.374, B:A.374, B:S.383 Water bridges: B:S.383 ACT.25: 4 residues within 4Å: Chain B: Q.203, S.204, I.208, F.212 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.212 Hydrogen bonds: B:S.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkinson, A.W. et al., SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Nature (2019)

Release Date

2018-12-19

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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