SMTL ID : 6mbl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: EDO.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:H.284, B:H.284, B:S.330 Water bridges: B:T.258, B:T.258 Salt bridges: B:R.80, B:R.259 pi-Stacking: B:F.332, B:F.332

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

EDO.2: 8 residues within 4Å: Chain B: P.46, E.51, E.54, H.209, F.212, S.213, K.216 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.54, B:S.213, B:K.216 EDO.3: 6 residues within 4Å: Chain A: D.15 Chain B: S.213, K.216, N.217, R.220 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.220, B:R.220 Water bridges: B:K.216 EDO.4: 8 residues within 4Å: Chain B: F.76, R.170, I.181, Q.182, L.184, P.185, S.186, W.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.170, B:R.170, B:I.181 EDO.5: 3 residues within 4Å: Chain B: E.109, F.334 Ligands: SAH.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.109, B:E.109 Water bridges: B:F.333 EDO.6: 3 residues within 4Å: Chain B: T.449, I.450, K.477 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.450 EDO.7: 4 residues within 4Å: Chain B: D.86, K.89, W.90, E.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.86, B:E.93 EDO.8: 1 residues within 4Å: Chain B: F.414 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: A.96, S.97, V.98, E.99, W.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.98, B:E.99 EDO.10: 2 residues within 4Å: Chain B: K.345, R.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.345, B:R.438 Water bridges: B:K.345 EDO.11: 6 residues within 4Å: Chain B: F.333, D.340, F.377, G.475, E.478, I.479 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.340, B:E.478, B:E.478

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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