SMTL ID : 6ox4.1 (1 other biounit)

A SETD3 Mutant (N255A) in Complex with an Actin Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: T.12, N.13 Chain B: M.157, G.158, N.159 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain B: K.454 Ligands: EDO.11 Ligand excluded by PLIP EDO.4: 11 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.7 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain B: D.210, A.324, E.325, H.329 Ligands: EDO.7 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain B: A.384, I.413, G.417 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain B: S.322, A.324, E.325, R.341, V.342, K.343 Ligands: EDO.4, EDO.5 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: L.457, H.460, D.461, L.462, K.467 Ligand excluded by PLIP EDO.9: 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.10: 7 residues within 4Å: Chain B: N.323, N.337, D.340, F.377, G.475, E.478, I.479 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: K.454, L.474, E.478 Ligands: EDO.3 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: I.30, Q.69, Y.226, S.243, F.244, T.245 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain B: S.370 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: R.59, T.60, E.63, E.196 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: F.333, V.464, K.467, M.468, K.471 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.405, G.406, D.407, S.408, A.409, R.412 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain B: D.407 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.20 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:H.284, B:H.284, B:G.331 Water bridges: B:E.108, 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.19: 4 residues within 4Å: Chain B: K.131, L.133, F.176, W.177 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.130, B:L.133 GOL.20: 6 residues within 4Å: Chain B: E.109, P.185, E.187, Y.188, D.189 Ligands: SAH.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.109, B:D.189 Water bridges: B:F.111, B:D.189, B:T.258 GOL.21: 6 residues within 4Å: Chain B: Q.206, I.344, K.345, L.346, R.438, L.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.206, B:K.345, B:R.438

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

ACT.22: 4 residues within 4Å: Chain B: V.372, F.373, A.374, S.383 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.374, B:S.383 ACT.23: 4 residues within 4Å: Chain B: Q.203, S.204, I.208, F.212 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.212 Hydrogen bonds: B:S.204 Water bridges: B:P.48, B:E.51

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
Actin-histidine N-methyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
A

Actin Peptide

Actin-histidine N-methyltransferase

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