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

SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First P212121 Crystal Form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 18 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 Ligands: GOL.9 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, B:G.331 Water bridges: B:R.80, B:E.108, B:E.109, B:E.109, B:D.189, B:T.258, B:T.258 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.2: 4 residues within 4Å: Chain B: P.48, E.51, I.208, F.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.48 Water bridges: B:T.205 EDO.3: 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.4: 4 residues within 4Å: Chain B: K.70, G.71, L.72, E.247 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.72 EDO.5: 3 residues within 4Å: Chain B: E.137, S.138, N.141 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.135, B:T.135, B:T.135 EDO.6: 7 residues within 4Å: Chain B: P.46, E.51, E.54, H.209, F.212, S.213, K.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.54, B:S.213, B:K.216 EDO.7: 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:K.471

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain B: N.323, F.333, D.340, F.377, G.475, E.478 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.323, B:E.478 Water bridges: B:N.336, B:E.478 GOL.9: 5 residues within 4Å: Chain B: E.109, P.185, E.187, Y.188 Ligands: SAH.1 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.109, B:E.187 Water bridges: B:F.111, B:D.189, B:D.189, B:T.258, B:T.258

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain B: R.200, Q.203, K.447 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.200, B:K.447, B:K.447, B:K.447, B:K.447 Salt bridges: B:R.200, B:K.447 SO4.11: 5 residues within 4Å: Chain B: F.373, A.374, H.376, S.383, Q.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.374, B:A.374, B:S.383

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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