SMTL ID : 6ox1.1 (1 other biounit)

SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.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 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:H.284, B:H.284 Water bridges: B:R.80, B:E.109, B:E.109, B:D.189, B:D.189, 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain B: K.454, L.457, E.478 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.478

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

EDO.3: 6 residues within 4Å: Chain B: D.210, A.324, E.325, I.328, H.329 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.210, B:H.329 EDO.4: 8 residues within 4Å: Chain B: Q.206, A.207, D.210, A.324, K.343, E.476 Ligands: EDO.3, EDO.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.210, B:D.210, B:K.343 EDO.5: 2 residues within 4Å: Chain B: D.82, D.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.82 EDO.6: 6 residues within 4Å: Chain B: I.30, Q.69, Y.226, S.243, F.244, T.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.69, B:F.244, B:F.244 EDO.7: 4 residues within 4Å: Chain B: F.84, P.85, E.102, M.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.103, B:M.103 EDO.8: 5 residues within 4Å: Chain B: F.333, V.464, K.467, M.468, K.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.464, B:M.468 EDO.9: 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.10: 5 residues within 4Å: Chain B: D.340, F.377, G.475, E.478, I.479 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.340, B:E.478 Water bridges: B:N.323, B:N.323, B:N.337 EDO.11: 6 residues within 4Å: Chain B: L.405, G.406, D.407, S.408, A.409, R.412 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.406, B:S.408, B:A.409, B:R.412, B:R.412 EDO.12: 5 residues within 4Å: Chain B: D.118, I.119, D.307, F.308, R.309 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain B: N.174, F.176 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.176 EDO.14: 5 residues within 4Å: Chain A: W.14, D.15 Chain B: I.153, R.220, Q.221 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.14, B:R.220, B:Q.221 EDO.15: 3 residues within 4Å: Chain B: M.88, K.89, S.92 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.89, B:S.92, B:S.92 EDO.16: 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.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.322, B:N.323, B:A.324 EDO.17: 3 residues within 4Å: Chain B: A.356, M.357, E.360 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.360

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, cytoplasmic 1: A
Histone-lysine N-methyltransferase setd3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
A

Actin, cytoplasmic 1

Histone-lysine N-methyltransferase setd3

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