SMTL ID : 6ox0.2 (1 other biounit)

SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 17 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, F.332, F.334 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:N.283, B:H.284, B:H.284, B:Y.318, B:G.331, A:H.8 Water bridges: B:R.80, B:E.109, B:E.109, B:D.189, B:T.258, B:R.259 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.2: 3 residues within 4Å: Chain B: A.365, Q.385, I.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.384 EDO.3: 4 residues within 4Å: Chain B: E.187, Y.188, D.189, R.465 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.188, B:R.465 Water bridges: B:E.187, B:D.189 EDO.4: 4 residues within 4Å: Chain B: L.346, G.347, F.393, R.438 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.345, B:G.347, B:R.438, B:R.438 EDO.5: 3 residues within 4Å: Chain B: H.339, R.341, H.376 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.339 Water bridges: B:S.338, B:S.338 EDO.6: 1 residues within 4Å: Chain B: D.297 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.297 EDO.7: 7 residues within 4Å: Chain A: I.6 Chain B: L.288, I.289, T.290, T.291, I.316, F.317 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.290, B:T.290, B:T.291, B:F.317, A:I.6 EDO.8: 5 residues within 4Å: Chain A: V.11 Chain B: T.320, R.321, E.325, R.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.320, B:R.341 EDO.9: 6 residues within 4Å: Chain B: P.46, E.51, E.54, F.212, S.213, K.216 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.54, B:S.213, B:K.216 Water bridges: B:E.54 EDO.10: 6 residues within 4Å: Chain B: F.333, D.335, V.464, K.467, M.468, K.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.333, B:V.464 EDO.11: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.69 Water bridges: B:G.71 EDO.12: 4 residues within 4Å: Chain B: D.340, F.377, G.475, E.478 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.340, B:E.478

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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