SMTL ID : 6ox4.2 (1 other biounit)

A SETD3 Mutant (N255A) in Complex with an Actin Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:F.111, B:F.111, B:N.283, B:H.284, B:H.284, B:Y.318, B:G.331 Water bridges: B:R.80, B:E.109, B:E.109, B:D.189, 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

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

EDO.2: 3 residues within 4Å: Chain B: A.365, A.384, I.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.413 Water bridges: B:G.417, B:G.417 EDO.3: 4 residues within 4Å: Chain B: F.333, V.464, M.468, K.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.333 Water bridges: B:F.333 EDO.4: 3 residues within 4Å: Chain B: R.66, K.67, Q.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.69 EDO.5: 3 residues within 4Å: Chain B: E.108, V.464 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.108 Water bridges: B:K.107, B:G.110 EDO.6: 4 residues within 4Å: Chain B: L.346, G.347, F.393, R.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.347, B:R.438, B:R.438 EDO.7: 3 residues within 4Å: Chain B: M.88, K.89, S.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.92 Water bridges: B:K.89, B:S.92 EDO.8: 8 residues within 4Å: Chain B: N.323, A.324, D.340, R.341, V.342, L.472, G.475, E.476 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.323, B:A.324, B:R.341, B:L.472 EDO.9: 3 residues within 4Å: Chain B: H.339, R.341, H.376 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.339 EDO.10: 5 residues within 4Å: Chain B: Q.69, Y.226, S.243, F.244, T.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.69, B:F.244 EDO.11: 4 residues within 4Å: Chain B: K.70, G.71, L.72, T.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.72 EDO.12: 7 residues within 4Å: Chain B: H.403, R.412, T.415, L.416, F.421, P.422, V.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.415, B:T.415 EDO.13: 3 residues within 4Å: Chain B: R.66, Y.193, R.250 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.63, B:R.250 Water bridges: B:R.59, B:R.465 EDO.14: 3 residues within 4Å: Chain B: L.124, W.127, R.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.299, B:R.299 EDO.15: 1 residues within 4Å: Chain B: S.370 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain B: D.189, R.465 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.465

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
Actin-histidine N-methyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

B
B

Actin Peptide

Actin-histidine N-methyltransferase

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