SMTL ID : 6ox0.1 (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

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

EDO.2: 2 residues within 4Å: Chain B: K.454, L.457 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain B: D.210, A.324, E.325, I.328, H.329 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain B: Q.206, A.207, D.210, A.324, K.343, E.476 Ligands: EDO.3, EDO.6 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain B: I.30, Q.69, Y.226, S.243, F.244 Ligand excluded by PLIP EDO.6: 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 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain B: L.346, G.347, F.393, R.438 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain B: P.85, E.102, M.103 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: F.333, V.464, K.467, M.468, K.471 Ligand excluded by PLIP EDO.10: 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.11: 6 residues within 4Å: Chain B: W.52, Q.203, S.204, I.208, H.209, F.212 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: K.107, E.108, V.464 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: V.372, F.373, A.374, S.383 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: D.335, N.336 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: L.124, W.127, R.299 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: M.88, K.89, S.92 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: 5 residues within 4Å: Chain B: Q.206, K.343, I.344, K.345, L.442 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: L.405, G.406, D.407, S.408, A.409, R.412 Ligand excluded by PLIP

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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