SMTL ID : 6wk2.1 (2 other biounits)

SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 residues within 4Å: Chain A: M.8 Chain B: R.75, E.103, E.104, F.106, P.180, T.253, R.254, D.275, M.276, C.277, N.278, H.279, Y.313, S.325, F.327, F.329 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:F.106, B:N.278, B:N.278, B:H.279, B:H.279, B:Y.313 Water bridges: B:E.104, B:E.104, B:D.184, B:D.184, B:T.253, B:T.253, B:S.325, B:G.326 Salt bridges: B:R.75, B:R.254 pi-Stacking: B:F.327, B:F.327 SAM.9: 17 residues within 4Å: Chain C: M.8 Chain D: R.75, E.103, E.104, F.106, P.180, T.253, R.254, D.275, M.276, C.277, N.278, H.279, Y.313, S.325, F.327, F.329 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:F.106, D:N.278, D:N.278, D:H.279, D:H.279 Water bridges: D:R.75, D:E.104, D:E.104, D:D.184, D:T.253, D:S.325, D:G.326 Salt bridges: D:R.75, D:R.254 pi-Stacking: D:F.327, D:F.327

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

EDO.2: 4 residues within 4Å: Chain B: K.102, E.103 Chain D: K.102 Ligands: EDO.5 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.102 Water bridges: B:K.102, B:G.105 EDO.3: 6 residues within 4Å: Chain B: I.25, Q.64, Y.221, S.238, F.239, T.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.64, B:S.238, B:F.239 EDO.4: 6 residues within 4Å: Chain B: L.400, G.401, D.402, S.403, A.404, R.407 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.401, B:S.403, B:A.404, B:R.407, B:R.407 EDO.5: 4 residues within 4Å: Chain B: E.103, K.462 Chain D: K.102 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.462 EDO.6: 5 residues within 4Å: Chain B: D.335, F.372, G.470, E.473, I.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.335, B:E.473 EDO.7: 4 residues within 4Å: Chain B: L.341, G.342, F.388, R.433 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.342, B:R.433, B:R.433 EDO.8: 4 residues within 4Å: Chain B: F.79, P.80, E.97, M.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.98, B:M.98 EDO.10: 4 residues within 4Å: Chain D: L.341, G.342, F.388, R.433 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.342, D:R.433, D:R.433

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain D: Q.198, S.199, I.203 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., Characterization of SETD3 methyltransferase-mediated protein methionine methylation. J.Biol.Chem. (2020)

Release Date

2020-06-17

Peptides

Actin, cytoplasmic 2: AC
Actin-histidine N-methyltransferase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

C
C

B
A

D
D

Actin, cytoplasmic 2

Actin-histidine N-methyltransferase

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