SMTL ID : 6wk1.1 (2 other biounits)

SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-2-2-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: T.12, N.13, K.19 Chain B: N.154 Ligands: EDO.31 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.154, B:N.154, A:N.13 Water bridges: B:G.153, B:G.153 GOL.4: 3 residues within 4Å: Chain B: K.126, F.171, W.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.126, B:K.126 GOL.5: 4 residues within 4Å: Chain B: I.339, K.340, R.433, L.437 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.340, B:R.433, B:R.433 GOL.6: 4 residues within 4Å: Chain B: Y.288, N.289, L.290, E.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.288, B:L.290, B:E.291, B:E.291 GOL.34: 1 residues within 4Å: Chain B: S.365 No protein-ligand interaction detected (PLIP) GOL.35: 1 residues within 4Å: Chain B: K.115 No protein-ligand interaction detected (PLIP)

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

EDO.2: 8 residues within 4Å: Chain A: Y.4, P.5, I.6 Chain B: Q.257, I.258, P.259, V.266 Ligands: EDO.33 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain B: K.449 Ligands: EDO.17 Ligand excluded by PLIP EDO.8: 10 residues within 4Å: Chain B: S.317, N.318, A.319, D.335, R.336, V.337, L.467, E.471 Ligands: EDO.10, EDO.14 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: D.205, A.319, E.320, I.323, H.324 Ligands: EDO.10, EDO.14 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain B: Q.201, A.202, D.205, A.319, K.338, E.471 Ligands: EDO.8, EDO.9, EDO.14 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: A.360, A.379, Q.380, A.383, I.408, G.412 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: G.73, D.77 Chain D: R.61, K.62, Q.64 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: D.113, I.114, K.115, D.302, F.303, R.304 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain B: S.317, A.319, E.320, R.336, V.337, K.338 Ligands: EDO.8, EDO.9, EDO.10 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: L.452, H.455, D.456, L.457, K.462 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: D.335, F.372, G.470, E.473, I.474 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: K.449, L.469, E.473 Ligands: EDO.7 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: P.41, E.49, H.204, S.208, K.211 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: R.61, K.62, Q.64 Chain D: D.72, G.73, D.77 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: I.25, Q.64, Y.221, S.238, F.239 Ligands: EDO.23 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: F.328, V.459, K.462, M.463, K.466 Ligands: EDO.25 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: L.400, G.401, D.402, S.403, A.404, R.407 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: Y.221, I.224, Q.225, L.235, K.236, D.237, S.238 Ligands: EDO.20 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: L.341, G.342, F.388, R.433 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: D.184, G.326, F.327, F.328, V.459, M.463 Ligands: EDO.21, EDO.54 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: L.67, S.181, E.182 Chain D: K.74 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: S.403, R.407 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: R.336, K.338, V.367, F.368, A.369 Ligands: ACT.26 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: F.429, D.432, R.433 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: Q.257, V.266, L.268 Ligands: GOL.1 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: F.79, P.80, E.97, M.98 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: P.5, I.6, E.7, I.10 Chain B: N.256, Q.257 Ligands: EDO.2 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: E.7 Chain D: I.284, G.314, T.315 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain D: A.360, I.408, F.409, L.411 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain D: E.182, Y.183, D.184 Ligands: EDO.45 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: K.102 Chain D: E.103, V.459 Ligands: EDO.49, EDO.50 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain D: L.341, G.342, F.388, R.433 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: M.83, K.84, S.87 Ligand excluded by PLIP EDO.43: 9 residues within 4Å: Chain D: S.317, N.318, A.319, D.335, R.336, L.467, G.470, E.471, I.474 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain D: H.334, R.336, H.371 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: P.180, S.181, E.182 Ligands: EDO.39 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: Q.64, Y.221, S.238, F.239 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain D: R.386, H.398, R.407, T.410, L.411, F.416, P.417, V.418 Ligand excluded by PLIP EDO.48: 2 residues within 4Å: Chain D: W.122, R.294 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain D: E.104, D.184, G.326, F.327, M.463 Ligands: SAH.36, EDO.40, EDO.50 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain D: F.327, F.328, V.459, M.463 Ligands: SAH.36, EDO.40, EDO.49 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: R.54, E.58, R.61, F.189, R.245 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain C: L.2 Chain D: T.285, G.287, E.296, V.298 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain D: L.400, G.401, D.402, S.403, A.404, R.407 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain B: K.102, E.103 Chain D: K.102 Ligands: EDO.25 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain D: Q.201, A.202, D.205, A.319, K.338 Ligand excluded by PLIP

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

SAH.3: 16 residues within 4Å: 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 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.106, B:F.106, B:N.278, B:H.279, B:H.279 Water bridges: B:R.75, B:E.104, B:E.104, B:E.104, 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 SAH.36: 18 residues within 4Å: 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 Ligands: EDO.49, EDO.50 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:F.106, D:F.106, D:N.278, D:H.279, D:H.279, D:Y.313 Water bridges: D:R.75, D:E.104, D:E.104, 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

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.26: 5 residues within 4Å: Chain B: F.368, A.369, S.378, Q.380 Ligands: EDO.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.369, B:S.378

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
Z

B
A

D
B

Actin, cytoplasmic 2

Actin-histidine N-methyltransferase

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